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spoc community resources update
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‎communities/spoc/lab/conclusion.html‎

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{% load markdown %}
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<!-- <section class="my-5">
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{% if help_links %}
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<h4 class="mb-3">{{ lab_name }} community support</h4>
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<ul>
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{% for link in help_links %}
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<li>
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<a href="{{ link.url }}" target="_blank">{{ link.title }}</a>
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</li>
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{% endfor %}
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</ul>
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{% endif %}
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</section>
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<section>
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<h4 class="mb-3">News and Events</h4>
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<div class="row justify-content-center">
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<div class="col">
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<iframe width="400px" height="600px" src="https://training.galaxyproject.org/training-material/topics/microbiome/feed.w.xml"></iframe>
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</div>
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<div class="col">
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<iframe width="400px" height="600px" src="https://training.galaxyproject.org/training-material/feeds/microbiome-month.w.xml"></iframe>
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</div>
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</div>
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</section> -->
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{% if feedback_email %}
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<section class="my-5">
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<h4 class="my-3">What do you think of the {{ lab_name }}?</h4>
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<button
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class="ga-btn"
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data-bs-toggle="modal"
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data-bs-target="#feedbackModal"
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>
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Give feedback
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</button>
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</section>
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{% endif %}
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<section class="my-5">
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<h4 class="mb-3">Cite Us</h4>
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</section>
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<section class="my-5">
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If you find the {{ lab_name }} Lab and the effort of the {{ lab_name }} community useful for your research, please cite us using this webpage.
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<!-- If you find the {{ lab_name }} Lab and the effort of the {{ lab_name }} community useful for your research, please cite us using our <a href="https://www.biorxiv.org/content/10.1101/2024.12.23.629682v1" target="_blank" rel="noopener noreferrer">preprint</a>-->
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</section>
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<section id="conclusionExtra">
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{{ conclusion_extra_md|safe }}
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</section>

‎communities/spoc/lab/intro.html‎

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<section class="my-5" id="tagline">
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<p>
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Welcome to the Galaxy {{ site_name }} {{ lab_name }} by the {{ lab_name }} community!
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</p>
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<p>
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#Here include an intro to your page, see the ex mple below from the microgalaxy community
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# Whether you're working with microbiome samples or bacterial isolates, long or short reads, shotgun or 16S sequencing, genomics, transcriptomics, proteomics, metabolomics, or integrative multi-omics analysis—this is the place for you! Learn more about the Microbiology Lab and the effort of the microGalaxy community in our <a href="https://www.biorxiv.org/content/10.1101/2024.12.23.629682v1" target="_blank" rel="noopener noreferrer">preprint</a>. </p>
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<p>
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<a
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href="#"
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data-bs-toggle="modal"
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data-bs-target="#infoModal">
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How does this page relate to Galaxy {{ site_name }}?
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</a>
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</p>
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{{ intro_extra_md }}
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<div class="modal fade" id="infoModal" tabindex="-1">
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<div class="modal-dialog modal-lg">
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<div class="modal-content">
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<div class="modal-header">
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<h5 class="modal-title">Galaxy {{ site_name }}</h5>
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<button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"></button>
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</div>
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<div class="modal-body">
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<p>
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This site <em>{{ subdomain }}.{{ root_domain }}</em> is connected to the same server as <em>{{ root_domain }}</em>, but with an interface dedicated to helping our {{ analysis_name }} researchers. Your history, jobs and data quota are shared with the "Base" Galaxy {{ site_name }} website.
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</p>
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<p><a class="ga-btn" href="https://{{ root_domain }}" target="_blank">Take me back to Galaxy {{ site_name }}</a></p>
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<p><a class="ga-btn" href="https://{{ root_domain }}/about">What is Galaxy {{ site_name }}?</a></p>
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<p><a class="ga-btn" href="{{support}}">Galaxy {{ site_name }} support</a></p>
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</div>
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<div class="modal-footer">
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<button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Close</button>
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</div>
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</div>
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</div>
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</div>
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</section>

‎communities/spoc/lab/sections/1_data_import_and_preparation.yml‎

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id: data
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title: Getting started
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tabs:
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- id: data-import
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title: Data import
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heading_md: >
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Common tools that allow for data import.
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content:
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- title_md: Import data to Galaxy
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description_md: >
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Standard upload of data to Galaxy, from your computer or from the web.
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button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=upload1"
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button_tip: Upload Data
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- title_md: Download data from NCBI GenBank/RefSeq
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description_md: >
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Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API
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button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fncbi_acc_download%2Fncbi_acc_download"
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button_tip: Download Data from NCBI
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- title_md: Download raw reads from NCBI SRA
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description_md: >
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Faster Download and Extract Reads in FASTQ format from NCBI SRA
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button_link: "{{ galaxy_base_url }}/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsra_tools%2Ffasterq_dump"
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button_tip: Download raw reads from NCBI SRA
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- title_md: Download run data from EBI SRA
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description_md: >
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ENA data can be searched and retrieved interactively and programmatically and visualized using this ENA Browser tool
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button_link: "https://www.ebi.ac.uk/ena/browser/search"
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button_tip: Download run data from EBI SRA
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- title_md: Download run data from UCSC
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description_md: >
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Use this tool to retrieve and export data from the Genome Browser annotation track database
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button_link: "https://genome.ucsc.edu/cgi-bin/hgTables"
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button_tip: Download run data from UCSC
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# - id: highlight-tools
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# title: Highlight tools
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# heading_md: >
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# Flagship tools for <your-community>
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# content:
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# - title_md: <code>Bakta</code> - Rapid and standardized annotation of bacterial genomes, MAGs and plasmids
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# description_md: >
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# A tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and Metagenomic Assembled Genomes (MAGs).
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# inputs:
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# - datatypes:
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# - fasta
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# button_link: "{{ galaxy_base_url }}/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/bakta/bakta"
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# - id: interactive-tools
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# title: Interactive tools
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# heading_md: >
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# Interactive tools for <your-community>
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# content:
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# - title_md: <code>Pavian</code> - Interactive analysis of metagenomics data
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# description_md: >
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# An interactive browser application for analyzing and visualization metagenomics classification results from classifiers such as Kraken, KrakenUniq, Kraken 2, Centrifuge and MetaPhlAn. Pavian also provides an alignment viewer for validation of matches to a particular genome.
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# inputs:
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# - datatypes:
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# - Kraken report
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# - MetaPhlAn report
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# button_link: "{{ galaxy_base_url }}/root?tool_id=interactive_tool_pavian"
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# - id: learning-pathways
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# title: Learning pathways
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# heading_md: >
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# Connected tutorials to train you to perform microbial data analysis.
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# content:
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# - title_md: Introduction to Galaxy and Sequence analysis
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# description_md: >
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# New to Galaxy and/or the field of genomics? In this learning pathway, you will learn how to use Galaxy for analysis, and will be guided through the most common first steps of any genome analysis; quality control and a mapping or assembly of your genomic sequences.
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# button_link: https://training.galaxyproject.org/training-material/learning-pathways/intro-to-galaxy-and-genomics.html
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# button_icon: tutorial
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# button_tip: Open Learning Pathway
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# heading_md: >
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# Connected tutorials to train you to perform microbial data analysis.

‎communities/spoc/lab/sections/2_tools.yml‎

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id: tools
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title: Community curated tools
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tabs:
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- id: clustering
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title: Clustering
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heading_md: 'Top 10 most used tools* for the EDAM operation: Clustering <br> *based
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on usage statistics from Galaxy’s main servers over the last five years'
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content:
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- title_md: gsc_scran_normalize
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description_md: |-
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Normalize raw counts using scran
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(Tool usage: 616)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=scran_normalize">scran_normalize</a></li>
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</ul>
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- title_md: infercnv
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description_md: |-
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Infer Copy Number Variation from Single-Cell RNA-Seq Data
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(Tool usage: 31)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=infercnv">infercnv</a></li>
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</ul>
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- title_md: gsc_filter_cells
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description_md: |-
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Filter single cell RNAseq data on library depth and number of detected genes
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(Tool usage: 0)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=filter_cells">filter_cells</a></li>
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</ul>
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- title_md: gsc_filter_genes
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description_md: |-
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Filter genes that are detected in less than a fraction of libraries in single cell RNAseq data
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(Tool usage: 0)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=filter_genes">filter_genes</a></li>
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</ul>
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- title_md: gsc_gene_expression_correlations
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description_md: |-
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Compute single-cell paire-wise gene expressions correlations
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(Tool usage: 0)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=single_cell_gene_expression_correlations">single_cell_gene_expression_correlations</a></li>
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</ul>
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- title_md: gsc_high_dimensions_visualisation
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description_md: |-
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Generates PCA, t-SNE and HCPC visualisation
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(Tool usage: 0)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=high_dimensions_visualisation">high_dimensions_visualisation</a></li>
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</ul>
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- title_md: gsc_mannwhitney_de
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description_md: |-
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Perform a mann-whitney differential testing between two sets of gene expression data
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(Tool usage: 0)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=mannwhitney_de">mannwhitney_de</a></li>
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</ul>
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- title_md: gsc_signature_score
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description_md: |-
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Compute signature scores from single cell RNAseq data
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(Tool usage: 0)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=signature_score">signature_score</a></li>
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</ul>
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- id: no_associated_edam_operation
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title: No associated EDAM operation
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heading_md: 'Top 10 most used tools* for the EDAM operation: No associated EDAM
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operation <br> *based on usage statistics from Galaxy’s main servers over the
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last five years'
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content:
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- title_md: volcanoplot
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description_md: |-
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Tool to create a Volcano Plot
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(Tool usage: 126750)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=volcanoplot">volcanoplot</a></li>
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</ul>
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- title_md: anndata
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description_md: |-
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Import, Export, Inspect and Manipulate Anndata and Loom objects
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(Tool usage: 87208)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=anndata_export">anndata_export</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=anndata_import">anndata_import</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=anndata_inspect">anndata_inspect</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=anndata_manipulate">anndata_manipulate</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=modify_loom">modify_loom</a></li>
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</ul>
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- title_md: seurat
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description_md: |-
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Seurat - R toolkit for single cell genomics
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(Tool usage: 10776)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=seurat_create">seurat_create</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=seurat_data">seurat_data</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=seurat_integrate">seurat_integrate</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=seurat_clustering">seurat_clustering</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=seurat_preprocessing">seurat_preprocessing</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=seurat_plot">seurat_plot</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=seurat_reduce_dimension">seurat_reduce_dimension</a></li>
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</ul>
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- title_md: sceasy
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description_md: |-
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Convert scRNA data object between popular formats
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(Tool usage: 2488)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=sceasy_convert">sceasy_convert</a></li>
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</ul>
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- title_md: deseq2_normalization
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description_md: |-
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Normalizes gene hitlists
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(Tool usage: 0)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=deseq2_normalization">deseq2_normalization</a></li>
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</ul>
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- id: rna-seq_analysis
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title: RNA-Seq analysis
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heading_md: 'Top 10 most used tools* for the EDAM operation: RNA-Seq analysis <br>
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*based on usage statistics from Galaxy’s main servers over the last five years'
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content:
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- title_md: deseq2
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description_md: |-
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Differential gene expression analysis based on the negative binomial distribution
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(Tool usage: 449489)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=deseq2">deseq2</a></li>
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</ul>
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- title_md: deg_annotate
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description_md: |-
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Annotate DESeq2/DEXSeq output tables
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(Tool usage: 79388)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=deg_annotate">deg_annotate</a></li>
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</ul>
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- title_md: crosscontamination_barcode_filter
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description_md: |-
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Barcode contamination discovery tool
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(Tool usage: 559)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=crosscontamination_barcode_filter">crosscontamination_barcode_filter</a></li>
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</ul>
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- title_md: velocyto
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description_md: |-
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Velocyto is a library for the analysis of RNA velocity.
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(Tool usage: 398)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=velocyto_cli">velocyto_cli</a></li>
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</ul>
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- id: visualisation
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title: Visualisation
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heading_md: 'Top 10 most used tools* for the EDAM operation: Visualisation <br>
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*based on usage statistics from Galaxy’s main servers over the last five years'
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content:
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- title_md: schicexplorer
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description_md: |-
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scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.
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(Tool usage: 2204)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicadjustmatrix">schicexplorer_schicadjustmatrix</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schiccluster">schicexplorer_schiccluster</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicclustercompartments">schicexplorer_schicclustercompartments</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicclusterminhash">schicexplorer_schicclusterminhash</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicclustersvl">schicexplorer_schicclustersvl</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicconsensusmatrices">schicexplorer_schicconsensusmatrices</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schiccorrectmatrices">schicexplorer_schiccorrectmatrices</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schiccreatebulkmatrix">schicexplorer_schiccreatebulkmatrix</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicdemultiplex">schicexplorer_schicdemultiplex</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicinfo">schicexplorer_schicinfo</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicmergematrixbins">schicexplorer_schicmergematrixbins</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicmergetoscool">schicexplorer_schicmergetoscool</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicnormalize">schicexplorer_schicnormalize</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicplotclusterprofiles">schicexplorer_schicplotclusterprofiles</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicplotconsensusmatrices">schicexplorer_schicplotconsensusmatrices</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=schicexplorer_schicqualitycontrol">schicexplorer_schicqualitycontrol</a></li>
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</ul>
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- title_md: scpipe
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description_md: |-
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A flexible preprocessing pipeline for single-cell RNA-sequencing data
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(Tool usage: 1443)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=scpipe">scpipe</a></li>
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</ul>
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- title_md: spapros
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description_md: |-
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Select and evaluate probe sets for targeted spatial transcriptomics.
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(Tool usage: 3)
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<ul>
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<li><a href="{{ galaxy_base_url }}/?tool_id=spapros_evaluation">spapros_evaluation</a></li>
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<li><a href="{{ galaxy_base_url }}/?tool_id=spapros_selection">spapros_selection</a></li>
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</ul>

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