diff crossSampleOverview.xml @ 2:a64ece32a01a draft default tip

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit a46097db0b6056e1125237393eb6974cfd51eb41"

--- a/crossSampleOverview.xml	Wed May 20 16:04:43 2020 -0400
+++ b/crossSampleOverview.xml	Tue Jul 28 08:32:36 2020 -0400
@@ -1,25 +1,23 @@
-<tool id="cross_sample_overview" name="Generate overview information" version="1.1+galaxy0">
+<tool id="cross_sample_overview" name="Generate overview information" version="1.1+galaxy1">
   <description>of a multi-sample analysis.</description>
   <requirements>
-    <requirement type="package" version="2.0.2">ig-flowtools</requirement>
+    <requirement type="package" version="1.0.5">pandas</requirement>
+    <requirement type="package" version="2.11.2">jinja2</requirement>
   </requirements>
   <stdio>
     <exit_code range="1" level="fatal" description="There are too many populations in the input files. The maximum number of populations is 40." />
     <exit_code range="2" level="fatal" description="There are populations inconsistencies between provided inputs." />
+    <exit_code range="3:"/>
   </stdio>
   <command><![CDATA[
-    mkdir templates &&
-    mkdir -p static/flowtools &&
-    mkdir -p static/images/flowtools &&
-    export FLOWTOOL='which crossSampleOverview.py' &&
-    FLOWTOOLDIR=\$(dirname $FLOWTOOL) &&
-    cp $FLOWTOOLDIR/../share/templates/* templates/ &&
-    cp -r $FLOWTOOLDIR/../share/static/flowtools/* static/flowtools/ &&
-    cp $FLOWTOOLDIR/../share/static/images/flowtools/* static/images/flowtools/ &&
-    crossSampleOverview.py -i '${input}' -I '${inputmfi}' -o '${html_file}' -m '${mfi}' -d '${html_file.files_path}' -t 'templates/'
+    python '$__tool_directory__/crossSampleOverview.py' -i '${input}' -I '${inputmfi}' -o '${html_file}' -m '${mfi}' -d '${html_file.files_path}' -t '$__tool_directory__'
     #for $f in $cs_outputs
        -s $f
     #end for
+    ;
+    cp -r '$__tool_directory__'/js '${html_file.files_path}/';
+    cp -r '$__tool_directory__'/css '${html_file.files_path}/';
+    cp -r '$__tool_directory__'/images '${html_file.files_path}/';
   ]]>
   </command>
   <inputs>
@@ -47,7 +45,7 @@
       <output name="html_file" file="out.html" compare="sim_size">
         <extra_files type="file" name="csAllMFIs.tsv" value="csAllMFIs.tsv"/>
         <extra_files type="file" name="csOverview.tsv" value="csOverview.tsv"/>
-        <extra_files type="file" name="csBoxplotData.json" value="csBoxplotData.json" compare="contains"/>
+        <extra_files type="file" name="csBoxplotData.json" value="csBoxplotData.json" compare="sim_size"/>
       </output>
     </test>
   </tests>