Biaftp update #1582
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,53 +1,55 @@ | ||
| <tool id="bia_download" name="FTP Link for Bioimage Archive" version="@VERSION@+galaxy0" profile="22.05"> | ||
| <description>Download images (TIFF) from Bioimage Archive</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="requirements" /> | ||
| <command detect_errors="aggressive"> | ||
| <![CDATA[ | ||
| curl -s https://www.ebi.ac.uk/biostudies/api/v1/studies/$accession/info | jq -r .ftpLink >> ftpLink.txt && | ||
| wget -q -r -l 0 -i ftpLink.txt && | ||
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|
||
| find . -type f -name "*.zip" | while read zip_file; do | ||
| unzip -o "\$zip_file" -d "\$(dirname "\$zip_file")" &> /dev/null; | ||
| done | ||
|
|
||
| ]]> | ||
| </command> | ||
| <inputs> | ||
| <param name="accession" type="text" label="The accession ID of BioImages-Core or BioStudies-JCB" help="for eg. S-BIAD570, S-JCBD-201309038"/> | ||
| <param name="ftplink_output" type="boolean" label="Generate FTP links?" help="If set, a file containing FTP links associated with the accession will be generated." /> | ||
| </inputs> | ||
| <outputs> | ||
| <collection name="images" type="list" label="${tool.name} on ${on_string}: TIFF Images"> | ||
| <discover_datasets pattern="(?P<designation>.*)\.tif" format="tif" directory="ftp.ebi.ac.uk" recurse="true" /> | ||
|
Owner
There was a problem hiding this comment. Do you know if the format is tiff or ome.tiff ?
Collaborator
Author
There was a problem hiding this comment. In the UI filtering options, it shows only tif as an option. I kept as it is. Btw, there are also several other image formats like lif, lsm, mrc and so on. I skipped them because there is no Galaxy datatype.
Owner
There was a problem hiding this comment. We can change the UI. The question is if the downloaded files are proper OME.tiff files. https://github.com/galaxyproject/galaxy/blob/5c686c62ecb5c23fa31ebae30db4f5a56c63630a/lib/galaxy/datatypes/images.py#L309
Collaborator
Author
There was a problem hiding this comment. how to check that?
Owner
There was a problem hiding this comment. |
||
| </collection> | ||
| <data format="txt" name="ftplinks" from_work_dir="ftpLink.txt" label="${tool.name} on ${on_string}: FTP Links"> | ||
| <filter>ftplink_output</filter> | ||
| </data> | ||
| </outputs> | ||
| <tests> | ||
| <test expect_num_outputs='1'> | ||
| <param name="accession" value="S-BIAD961" /> | ||
| <param name="ftplink_output" value="False" /> | ||
| <output_collection name="images"> | ||
| <element name="Study_Component-4_mznanog_mCherry-AAT"> | ||
| <assert_contents><has_size value="14092624" /></assert_contents> | ||
| </element> | ||
| </output_collection> | ||
| </test> | ||
| <test expect_num_outputs='2'> | ||
| <param name="accession" value="S-JCBD-201309038" /> | ||
| <param name="ftplink_output" value="True" /> | ||
| <output_collection name="images"> | ||
| <element name="JCB_STIL_serial"> | ||
| <assert_contents><has_size value="7446240" /></assert_contents> | ||
| </element> | ||
| <element name="Sir_JCB_STIL_serial"> | ||
| <assert_contents><has_size value="7436060" /></assert_contents> | ||
| </element> | ||
| </output_collection> | ||
| <output name="ftplinks" ftype="txt" file="ftpLink.txt" lines_diff="0" /> | ||
| </test> | ||
| </tests> | ||
| <help> | ||
| <
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1 @@ | ||
| ftp://ftp.ebi.ac.uk/biostudies/fire/S-JCBD-/S-JCBD-xxx038/S-JCBD-201309038 |
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How do we make sure that we only get tif files?
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We get the whole ftp directory of that accession.
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There is no particular directory structure. So I download everything and filter for tif later.
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Can you not filter this file first, instead of downloading everything and throwing that away later?