Merge pull request #1611 from pavanvidem/biaftp-tif-to-tiff

biaftp change from tif to tiff

Author: bgruening

tools/image_processing/bia-ftplinks/biaftplink.xml

@@ -1,4 +1,4 @@
-<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>
@@ -7,7 +7,7 @@
     <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 -A "*.tif,*.png,*.jpg,*.zip" -i ftpLink.txt &&
+    wget -q -r -l 0 -A "*.tiff,*.tif,*.png,*.jpg,*.zip" -i ftpLink.txt &&
 
     find . -type f -name "*.zip" | while read zip_file; do
         unzip -o "\$zip_file" -d "\$(dirname "\$zip_file")";
@@ -20,8 +20,9 @@
         <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="tif_images" type="list" label="${tool.name} on ${on_string}: TIF Images">
-            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.tif" format="tif" directory="ftp.ebi.ac.uk" recurse="true" />
+        <collection name="tiff_images" type="list" label="${tool.name} on ${on_string}: TIFF Images">
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.tiff" format="tiff" directory="ftp.ebi.ac.uk" recurse="true" />
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.tif" format="tiff" directory="ftp.ebi.ac.uk" recurse="true" />
         </collection>
         <collection name="png_images" type="list" label="${tool.name} on ${on_string}: PNG Images">
             <discover_datasets pattern="(?P&lt;designation&gt;.*)\.png" format="png" directory="ftp.ebi.ac.uk" recurse="true" />
@@ -37,7 +38,7 @@
         <test expect_num_outputs='3'>
             <param name="accession" value="S-BIAD961" />
             <param name="ftplink_output" value="False" />
-            <output_collection name="tif_images" type="list" count="1">
+            <output_collection name="tiff_images" type="list" count="1">
                 <element name="Study_Component-4_mznanog_mCherry-AAT">
                     <assert_contents><has_size value="14092624" /></assert_contents>
                 </element>
@@ -46,7 +47,7 @@
         <test expect_num_outputs='4'>
             <param name="accession" value="S-JCBD-201309038" />
             <param name="ftplink_output" value="True" />
-            <output_collection name="tif_images" type="list" count="2">
+            <output_collection name="tiff_images" type="list" count="2">
                  <element name="JCB_STIL_serial">
                     <assert_contents><has_size value="7446240" /></assert_contents>
                 </element>
@@ -81,7 +82,7 @@
     <help>
 <![CDATA[
         **What it does**
-        This tool downloads images from the Bioimage Archive and optionally outputs FTP links associated with the input accession. The tools currently supports downloading TIF, PNG and JPG formats that are supported by Galaxy.
+        This tool downloads images from the Bioimage Archive and optionally outputs FTP links associated with the input accession. The tools currently supports downloading TIFF, PNG and JPG formats that are supported by Galaxy.
 ]]>
     </help>
     <expand macro="citations" />