[BH2024] Update Bioimaging Archive retrieval tool

tools/image_processing/bia-ftplinks/.shed.yml

@@ -2,9 +2,11 @@ name: bia_download
 owner: bgruening
 categories:
   - Imaging
-description: Tool to query ftp links for study from bioimage archive
+description: Tool to query FTP links for studies from the BioImage Archive
+long_description: A wrapper that wget's FTP links for studies from the BioImage Archive (https://www.ebi.ac.uk/bioimage-archive/). 
+homepage_url: https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks
 remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools
 type: unrestricted
 auto_tool_repositories:
   name_template: "{{ tool_id }}"
-  description_template: "A Tool to query ftp links by study name(s) from bioimage archive."
+  description_template: "A tool to query FTP links by study name(s) from the BioImage Archive."

tools/image_processing/bia-ftplinks/biaftplink.xml

@@ -1,22 +1,36 @@
-<tool id="bia_download" name="FTP Link for Bioimage Archive" version="@VERSION@+galaxy0" profile="22.05">
-    <description>Download images from Bioimage Archive</description>
+<tool id="bia_download" name="FTP Link for BioImage Archive" version="@VERSION@+galaxy1" profile="23.0">
+    <description>Download images from BioImage Archive</description>
     <macros>
         <import>macros.xml</import>
     </macros>
+        <edam_topics>
+        <edam_topic>topic_3383</edam_topic>
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_2422</edam_operation>
+    </edam_operations>
     <expand macro="requirements" />
     <command detect_errors="aggressive">
 <![CDATA[
-        wget -r 'ftp://ftp.ebi.ac.uk/biostudies/$mode/$path'/Files; 
+        #set $accession = str($path)
+        #if $accession.startswith('S-BIAD') and '/' not in $accession
+        #set $accession_number = $accession[6:]
+        #set $accession = 'S-BIAD/' + $accession_number + '/' + $accession
+        #end if
+        wget -r 'ftp://ftp.ebi.ac.uk/biostudies/$mode/$accession'/Files; 
         #if '$ftp_output'
             #set study = $path.split('/')[-1].rstrip('/')
             curl https://www.ebi.ac.uk/biostudies/api/v1/studies/$study/info -s |jq -r .ftpLink >>ftpLink.txt
         #end if
 ]]>
     </command>
     <inputs>
-    <param name="mode" type="text" label="Storage mode" help="The storage mode, can be either nfs or fire."/>
-    <param name="path" type="text" label="The path of accession. e.g. S-BIAD/570/S-BIAD570 "/>
-        <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." />
+        <param name="mode" type="select" label="Storage mode" help="FIRE (default) or NFS. See help section below for more information." optional="false">
+            <option value="fire" selected="true">FIRE</option>
+            <option value="nfs">NFS</option>
+        </param>
+        <param name="path" type="text" label="Accession number or path (e.g. S-BIAD570 or S-BIAD/570/S-BIAD570)" optional="false" help="All publically available data in the BioImage Archive (from the Bioimages - Core collection) is accessible &lt;a href='https://www.ebi.ac.uk/biostudies/BioImages/studies' target='_blank'&gt;here&lt;/a&gt;. Each study is associated with a unique accession number e.g. S-BIAD570."/>
+        <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>
         <data name="images" format="tiff">
@@ -51,9 +65,21 @@
     </tests>
     <help>
 <![CDATA[
-        **What it does**
+    **What it does**  
+
         This tool downloads images from the Bioimage Archive and optionally outputs FTP links associated with the input accession.
+
+    **Additional help**    
+
+    - Storage mode  
+        FIle REplication or FIRE is EMBL-EBI's very large-scale object data storage system. At the moment of writing, all their studies have been migrated to FIRE storage. This is why it is the default option. However, they are introducing a new feature that will use NFS as a storage option (again), so the data you want to download might live on NFS in the near future. This is the reason both options are available.  
+
+
+    - Accession number  
+        This tool only supports studies part of the 'BioImages - Core' collection, which can be recongized by having an accession number that follows the 'S-BIAD000' pattern. Providing the whole path is also suported (e.g. S-BIAD/000/S-BIAD000).
+
+
 ]]>
     </help>
     <expand macro="citations" />
-</tool>
+</tool>

tools/image_processing/bia-ftplinks/macros.xml

@@ -11,7 +11,7 @@
     <xml name="citations">
         <citations>
             <citation type="bibtex">
-                @misc{bia,,
+                @misc{bia,
                  title = "BioImage Archive Downloading via ftp",                 
                  note = "https://www.ebi.ac.uk/bioimage-archive/help-download/",
                  url = "https://www.ebi.ac.uk/bioimage-archive/help-download/"}</citation>