biodiversity community automatic resources update

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

@@ -1,6 +1,17 @@
 id: tools
 title: Tools
 tabs:
+- id: request_tools
+  title: Request tools
+  heading_md: Request a new tools or look at the complete list
+  content:
+  - title_md: Request a new tool or installation of tool
+    description_md: If one of the tools listed here can not be open, it means it
+      is not installed on this server. Please contact the <a href="{{ support 
+      }}">support</a>.
+  - title_md: See the complete tool list
+    description_md: Our comprehensive curated tool list is available via <a 
+      href="https://galaxyproject.github.io/galaxy_codex/communities/biodiversity/resources/">https://galaxyproject.github.io/galaxy_codex/communities/biodiversity/resources/</a>.
 - id: de-novo_assembly
   title: De-novo assembly
   heading_md: 'Top 10 most used tools* for the EDAM operation: De-novo assembly <br>
@@ -124,6 +135,13 @@ tabs:
       <ul>
         <li><a href="{{ galaxy_base_url }}/?tool_id=helixer">helixer</a></li>
       </ul>
+  - title_md: tiberius
+    description_md: |-
+      Tiberius is a tool for deep learning-based ab initio gene structure prediction
+       (Tool usage: 0)
+      <ul>
+        <li><a href="{{ galaxy_base_url }}/?tool_id=tiberius">tiberius</a></li>
+      </ul>
   - title_md: vcontact2
     description_md: |-
       Tool to provide taxonomic context of metagenomic sequencing data
@@ -448,14 +466,3 @@ tabs:
         <li><a href="{{ galaxy_base_url }}/?tool_id=fastk_histex">fastk_histex</a></li>
         <li><a href="{{ galaxy_base_url }}/?tool_id=fastk_logex">fastk_logex</a></li>
       </ul>
-- id: request_tools
-  title: Request tools
-  heading_md: Request a new tools or look at the complete list
-  content:
-  - title_md: Request a new tool or installation of tool
-    description_md: If one of the tools listed here can not be open, it means it
-      is not installed on this server. Please contact the <a href="{{ support 
-      }}">support</a>.
-  - title_md: See the complete tool list
-    description_md: Our comprehensive curated tool list is available via <a 
-      href="https://galaxyproject.github.io/galaxy_codex/communities/biodiversity/resources/">https://galaxyproject.github.io/galaxy_codex/communities/biodiversity/resources/</a>.

communities/biodiversity/lab/sections/3_workflows.yml

@@ -63,91 +63,92 @@ tabs:
       https://training.galaxyproject.org/training-material/faqs/galaxy/workflows_import.html
   - title_md: Galaxy Workflow ERGA-BGE Genome Report ASM analyses (one-asm Long 
       Reads + HiC)
-    description_md: Workflow covering operations related to Mapping,Data 
-      deposition,Genome assembly,Scaffolding,Sequence alignment analysis,k-mer 
-      counting,Sequence assembly validation,Pairwise sequence alignment,Data 
-      retrieval,Sequence database search,Visualisation,De-novo 
-      assembly,Phasing,Data parsing,Genotyping,Data handling,Sequence trimmingon
-      topics related to Genomics
+    description_md: Workflow covering operations related to 
+      Visualisation,Sequence alignment analysis,Sequence trimming,Data 
+      deposition,Mapping,Phasing,Genotyping,k-mer counting,Data 
+      handling,Scaffolding,Sequence database search,Data parsing,De-novo 
+      assembly,Pairwise sequence alignment,Data retrieval,Sequence assembly 
+      validation,Genome assemblyon topics related to Genomics
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1104'
     button_tip: View workflow
     button_icon: view
   - title_md: ERGA Long reads+HiC Assembly+QC Hifiasm v2602 (WF2)
-    description_md: Workflow covering operations related to Data 
-      handling,Sequence assembly visualisation,Genome assembly,De-novo 
-      assembly,Phasing,Scaffolding,k-mer counting,Sequence assembly validationon
-      topics related to Whole genome sequencing
+    description_md: Workflow covering operations related to Phasing,Sequence 
+      assembly visualisation,Scaffolding,Sequence assembly validation,Genome 
+      assembly,De-novo assembly,k-mer counting,Data handlingon topics related to
+      Whole genome sequencing
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=605'
     button_tip: View workflow
     button_icon: view
   - title_md: ERGA Profiling Long Reads v2602 (WF1)
-    description_md: Workflow covering operations related to Genotyping,k-mer 
-      counting,Sequence trimmingon topics related to Whole genome sequencing
+    description_md: Workflow covering operations related to k-mer 
+      counting,Sequence trimming,Genotypingon topics related to Whole genome 
+      sequencing
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=603'
     button_tip: View workflow
     button_icon: view
   - title_md: ERGA DataQC HiFi v2601 (WF0)
-    description_md: Workflow covering operations related to Sequence 
-      conversion,Read pre-processing,DNA transcription,Sequence 
-      trimming,Sequencing quality control,DNA translation,Primer 
-      removal,Sequence composition calculation,Validation,Statistical 
-      calculationon topics related to Whole genome sequencing
+    description_md: Workflow covering operations related to Primer 
+      removal,Sequence trimming,Read pre-processing,DNA translation,Sequence 
+      composition calculation,DNA transcription,Sequence 
+      conversion,Validation,Statistical calculation,Sequencing quality controlon
+      topics related to Whole genome sequencing
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=602'
     button_tip: View workflow
     button_icon: view
   - title_md: ERGA DataQC Illumina v2601 (WF0)
     description_md: Workflow covering operations related to Sequence 
-      conversion,Sequence contamination filtering,DNA transcription,Sequence 
-      trimming,Sequencing quality control,DNA translation,Sequence composition 
-      calculation,Validation,Statistical calculationon topics related to Whole 
-      genome sequencing
+      trimming,Sequence contamination filtering,DNA translation,Sequence 
+      composition calculation,DNA transcription,Sequence 
+      conversion,Validation,Statistical calculation,Sequencing quality controlon
+      topics related to Whole genome sequencing
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=601'
     button_tip: View workflow
     button_icon: view
   - title_md: ERGA DataQC ONT v2505 (WF0)
-    description_md: Workflow covering operations related to DNA 
-      translation,Sequence conversion,Scatter plot plotting,Box-Whisker plot 
-      plotting,DNA transcription,Sequence trimmingon topics related to Whole 
-      genome sequencing
+    description_md: Workflow covering operations related to Sequence 
+      trimming,Sequence conversion,Box-Whisker plot plotting,DNA 
+      translation,Scatter plot plotting,DNA transcriptionon topics related to 
+      Whole genome sequencing
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=697'
     button_tip: View workflow
     button_icon: view
   - title_md: ERGA Long Reads PriAlt Purge+QC v2505 (WF3)
-    description_md: Workflow covering operations related to Data handling,Genome
-      assembly,k-mer counting,Read binning,Sequence assembly validation,Pairwise
-      sequence alignment,De-novo assembly,Scaffolding,Phasingon topics related 
-      to Whole genome sequencing
+    description_md: Workflow covering operations related to Scaffolding,De-novo 
+      assembly,Phasing,Pairwise sequence alignment,Sequence assembly 
+      validation,Genome assembly,Read binning,k-mer counting,Data handlingon 
+      topics related to Whole genome sequencing
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1163'
     button_tip: View workflow
     button_icon: view
   - title_md: ERGA HiC Pri Scaffolding+QC YaHS v2505 (WF4)
-    description_md: Workflow covering operations related to Data handling,Genome
-      assembly,De-novo assembly,Phasing,Scaffolding,k-mer counting,Sequence 
-      assembly validation,Sequence alignmenton topics related to Whole genome 
-      sequencing
+    description_md: Workflow covering operations related to Sequence 
+      alignment,Scaffolding,De-novo assembly,Phasing,Sequence assembly 
+      validation,Genome assembly,k-mer counting,Data handlingon topics related 
+      to Whole genome sequencing
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1164'
     button_tip: View workflow
     button_icon: view
   - title_md: ERGA Long reads-only Assembly+QC Hifiasm v2505 (WF2)
-    description_md: Workflow covering operations related to Data 
-      handling,Sequence assembly visualisation,Genome assembly,De-novo 
-      assembly,Phasing,Scaffolding,k-mer counting,Sequence assembly validationon
-      topics related to Whole genome sequencing
+    description_md: Workflow covering operations related to Phasing,Sequence 
+      assembly visualisation,Scaffolding,Sequence assembly validation,Genome 
+      assembly,De-novo assembly,k-mer counting,Data handlingon topics related to
+      Whole genome sequencing
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1162'
     button_tip: View workflow
     button_icon: view
   - title_md: ERGA-BGE Genome Report ANNOT analyses
-    description_md: Workflow covering operations related to Differential protein
-      expression profiling,Data handling,Genome annotation,Sequence assembly 
-      validationon topics related to Genomics
+    description_md: Workflow covering operations related to Genome 
+      annotation,Differential protein expression profiling,Sequence assembly 
+      validation,Data handlingon topics related to Genomics
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1096'
     button_tip: View workflow
     button_icon: view
   - title_md: Genome assembly workflow for nanopore reads, for TSI
-    description_md: Workflow covering operations related to Sequence assembly 
-      visualisation,Genome assembly,Sequencing quality control,De-novo 
-      assembly,Cross-assembly,Mapping assembly,Sequence composition 
-      calculation,Statistical calculation
+    description_md: Workflow covering operations related to Sequencing quality 
+      control,Cross-assembly,Sequence assembly visualisation,Sequence 
+      composition calculation,De-novo assembly,Genome assembly,Statistical 
+      calculation,Mapping assembly
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1114'
     button_tip: View workflow
     button_icon: view
@@ -157,18 +158,18 @@ tabs:
     button_tip: View workflow
     button_icon: view
   - title_md: ERGA HiC Collapsed Scaffolding+QC YaHS v2311 (WF4)
-    description_md: Workflow covering operations related to Data handling,Genome
-      assembly,De-novo assembly,Phasing,Scaffolding,k-mer counting,Sequence 
-      assembly validation,Sequence alignmenton topics related to Whole genome 
+    description_md: Workflow covering operations related to Phasing,Sequence 
+      alignment,Scaffolding,Sequence assembly validation,Genome assembly,De-novo
+      assembly,k-mer counting,Data handlingon topics related to Whole genome 
       sequencing
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=702'
     button_tip: View workflow
     button_icon: view
   - title_md: ERGA ONT+Illumina Collapsed Purge+QC v2311 (WF3)
-    description_md: Workflow covering operations related to Data handling,Genome
-      assembly,k-mer counting,Read binning,Sequence assembly validation,Pairwise
-      sequence alignment,De-novo assembly,Scaffolding,Phasingon topics related 
-      to Whole genome sequencing
+    description_md: Workflow covering operations related to Scaffolding,De-novo 
+      assembly,Phasing,Pairwise sequence alignment,Sequence assembly 
+      validation,Genome assembly,Read binning,k-mer counting,Data handlingon 
+      topics related to Whole genome sequencing
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=701'
     button_tip: View workflow
     button_icon: view
@@ -178,9 +179,9 @@ tabs:
     button_tip: View workflow
     button_icon: view
   - title_md: ERGA HiC Hap1Hap2 Scaffolding+QC YaHS v2309 (WF4)
-    description_md: Workflow covering operations related to Data handling,Genome
-      assembly,De-novo assembly,Phasing,Scaffolding,k-mer counting,Sequence 
-      assembly validation,Sequence alignmenton topics related to Whole genome 
+    description_md: Workflow covering operations related to Phasing,Sequence 
+      alignment,Scaffolding,Sequence assembly validation,Genome assembly,De-novo
+      assembly,k-mer counting,Data handlingon topics related to Whole genome 
       sequencing
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=608'
     button_tip: View workflow
@@ -221,15 +222,15 @@ tabs:
     button_tip: View workflow
     button_icon: view
   - title_md: Metagenomics assembly tutorial workflow
-    description_md: Workflow covering operations related to Visualisation,Genome
-      assembly,Sequence assembly visualisation,Read mapping,Sequence assembly 
-      validation
+    description_md: Workflow covering operations related to 
+      Visualisation,Sequence assembly validation,Genome assembly,Sequence 
+      assembly visualisation,Read mapping
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1634'
     button_tip: View workflow
     button_icon: view
   - title_md: Genome Annotation with Prokka
-    description_md: Workflow covering operations related to Coding region 
-      prediction,Genome annotation,Genome visualisation,Gene prediction
+    description_md: Workflow covering operations related to Genome 
+      annotation,Genome visualisation,Gene prediction,Coding region prediction
     button_link: '{{ galaxy_base_url }}/workflows/trs_import?trs_server=workflowhub.eu&run_form=true&trs_id=1497'
     button_tip: View workflow
     button_icon: view
@@ -261,8 +262,8 @@ tabs:
     button_tip: View workflow
     button_icon: view
   - title_md: Obitools eDNA metabarcoding
-    description_md: Workflow covering operations related to Sequencing quality 
-      control,Sequence composition calculation,Statistical calculation
+    description_md: Workflow covering operations related to Statistical 
+      calculation,Sequencing quality control,Sequence composition calculation
     button_link: https://usegalaxy.eu/published/workflow?id=afad9a17a80bb26d
     button_tip: View workflow
     button_icon: view
@@ -293,18 +294,18 @@ tabs:
     button_tip: View workflow
     button_icon: view
   - title_md: 16S_biodiversity_for_nonoverlap_paired_end
-    description_md: Workflow covering operations related to Formatting,Read 
-      mapping,Generation,Sequence alignment,Sequencing quality control,DNA 
-      mapping,Chimera detection,Sequence composition calculation,Genome 
-      indexing,Statistical calculation
+    description_md: Workflow covering operations related to Sequencing quality 
+      control,Sequence alignment,Chimera detection,Formatting,Sequence 
+      composition calculation,DNA mapping,Generation,Statistical 
+      calculation,Genome indexing,Read mapping
     button_link: https://usegalaxy.org.au/published/workflow?id=869440d35a618836
     button_tip: View workflow
     button_icon: view
   - title_md: 16S_biodiversity_for_overlap_paired_end
-    description_md: Workflow covering operations related to Formatting,Read 
-      mapping,Sequence merging,Generation,Sequence alignment,Sequencing quality 
-      control,DNA mapping,Chimera detection,Sequence composition 
-      calculation,Genome indexing,Statistical calculation
+    description_md: Workflow covering operations related to Sequencing quality 
+      control,Sequence alignment,Chimera detection,Formatting,Sequence 
+      composition calculation,DNA mapping,Generation,Statistical 
+      calculation,Genome indexing,Sequence merging,Read mapping
     button_link: https://usegalaxy.org.au/published/workflow?id=14e80b7f9f68ec2a
     button_tip: View workflow
     button_icon: view