Biaftp update

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

@@ -3,6 +3,9 @@ owner: bgruening
 categories:
   - Imaging
 description: Tool to query ftp links for study from bioimage archive
+long_description: |
+  Tool to query ftp links for study from bioimage archive.
+homepage_url: https://www.ebi.ac.uk/biostudies/bioimages/studies
 remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools
 type: unrestricted
 auto_tool_repositories:

tools/image_processing/bia-ftplinks/biaftplink.xml

@@ -1,27 +1,31 @@
-<tool id="bia_download" name="FTP Link for Bioimage Archive" version="@VERSION@+galaxy0" profile="22.05">
+<tool id="bia_download" name="FTP Link for Bioimage Archive" version="@VERSION@+galaxy1" profile="22.05">
     <description>Download images from Bioimage Archive</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <command detect_errors="aggressive">
 <![CDATA[
-        wget -r 'ftp://ftp.ebi.ac.uk/biostudies/$mode/$path'/Files; 
+        wget -r 'ftp://ftp.ebi.ac.uk/biostudies/$mode/$path'/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="mode" type="select" label="Storage mode" help="The storage mode, can be either nfs or fire.">
+        <option value="fire">fire</option>
+        <option value="nfs">nfs</option>
+    </param>
     <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." />
     </inputs>
     <outputs>
-        <data name="images" format="tiff">
-            <discover_datasets pattern="__name_and_ext__" format="tif,tiff" directory="ftp.ebi.ac.uk" visible="true" recurse="true" />
-        </data>
+        <collection name="images" type="list" label="TIFF Images">
+
+            <discover_datasets pattern="__name_and_ext__" format="tif,tiff" directory="ftp.ebi.ac.uk" recurse="true" />
+        </collection>
         <data format="txt" name="ftplinks" from_work_dir="ftpLink.txt" label="FTP Links">
             <filter>ftplink_output</filter>
         </data>
@@ -31,21 +35,21 @@
             <param name="mode" value="fire" />
             <param name="path" value="S-BIAD/961/S-BIAD961" />
             <param name="ftplink_output" value="False" />
-            <output name="images">
-                <discovered_dataset designation="Study_Component-4_mznanog_mCherry-AAT" ftype="tif">
-                    <assert_contents><has_size value="14092624" /></assert_contents>
-                </discovered_dataset>
-            </output>
+            <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="mode" value="fire" />
             <param name="path" value="S-BIAD/961/S-BIAD961" />
             <param name="ftplink_output" value="True" />
-            <output name="images">
-                 <discovered_dataset designation="Study_Component-4_mznanog_mCherry-AAT" ftype="tif">
+            <output_collection name="images">
+                 <element name="Study_Component-4_mznanog_mCherry-AAT">
                      <assert_contents><has_size value="14092624" /></assert_contents>
-                </discovered_dataset>
-            </output>
+                </element>
+            </output_collection>
                <output name="ftplinks" ftype="txt" file="ftpLink.txt" lines_diff="0" />
             </test>
     </tests>