diff hicPlotViewpoint.xml @ 7:5e9c304c424c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"

--- a/hicPlotViewpoint.xml	Mon Dec 16 08:54:06 2019 -0500
+++ b/hicPlotViewpoint.xml	Mon Dec 16 15:42:31 2019 -0500
@@ -7,12 +7,12 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
 
-        #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
-            ln -s '$m' ${counter}_matrix &&
+       #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
+            ln -s '$m' ${counter}_matrix.$m.ext &&
         #end for
-        #set $m = '" "'.join([ '%s_matrix' % $counter for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
-
-        hicPlotViewpoint --matrix "$m"
+        #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
+       
+        @BINARY@ --matrix $m
         #if $interactionOutFileName:
             $interactionOutFileName interactions
         #end if
@@ -20,10 +20,11 @@
         --region $region
         --referencePoint $referencePoint
         && mv plot.$image_file_format plot
-        && ls -lah
+        
         #if $interactionOutFileName:
-            #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
-                && mv interactions_${counter}_matrix.bedgraph ${counter}_interactions.bedgraph
+            && mkdir interaction 
+            #for $counter, $matrix in enumerate($m.split(' ')):
+                && mv interactions_${matrix}.bedgraph interaction/${counter}_interactions.bedgraph
             #end for
         #end if
 ]]>
@@ -52,28 +53,28 @@
         </data>
 
         <data format="bedgraph" name="interactionFile" >
-            <discover_datasets pattern='(?P&lt;designation&gt;.+)\_interactions\.bedgraph' directory="." visible="true"/>
             <filter>interactionOutFileName</filter>
+            <discover_datasets pattern='__name_and_ext__' directory="interaction" visible="true"/>
         </data>
 
     </outputs>
     <tests>
         <test>
-            <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
+            <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.cool"/>
             <param name="image_file_format" value="png" />
             <param name='region' value='X:3000000-3500000' />
             <param name='referencePoint' value='X:3200000' />
             <output name="outFileName" file="li_viewpoint_32Mb.png" ftype="png" compare="sim_size"/>
         </test>
         <test>
-            <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
+            <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.cool"/>
             <param name="image_file_format" value="png" />
             <param name='region' value='X:3000000-3500000' />
             <param name='referencePoint' value='X:3200000-3300000' />
             <param name='interactionOutFileName' value='True' />
             <output name="outFileName" file="li_viewpoint_32-33Mb.png" ftype="png" compare="sim_size"/>
             <output name="interactionFile">
-                <discovered_dataset designation="0" file="li_32-33mb_interactions.bedgraph" />
+                <discovered_dataset designation="0_interactions" file="li_32-33mb_interactions.bedgraph" />
             </output>
         </test>
     </tests>