Mercurial > repos > bgruening > deeptools

diff computeMatrix.xml @ 66:1dbd76a58d8b draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
author galaxyp
date Sat, 30 May 2015 13:55:46 -0400
parents 9bee2c86eeb1
children
line wrap: on
line diff
--- a/computeMatrix.xml	Mon May 25 05:16:10 2015 -0400
+++ b/computeMatrix.xml	Sat May 30 13:55:46 2015 -0400
@@ -63,13 +63,13 @@
                 $advancedOpt.skipZeros
                 --binSize $advancedOpt.binSize
 
-                #if $advancedOpt.minThreshold:
+                #if $advancedOpt.minThreshold is not None and str($advancedOpt.minThreshold) != '':
                     --minThreshold $advancedOpt.minThreshold
                 #end if
-                #if $advancedOpt.maxThreshold:
+                #if $advancedOpt.maxThreshold is not None and str($advancedOpt.maxThreshold) != '':
                     --maxThreshold $advancedOpt.maxThreshold
                 #end if
-                #if $advancedOpt.scale:
+                #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '':
                     --scale $advancedOpt.scale
                 #end if
 
@@ -223,7 +223,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="deeptools_matrix" name="outFileName" label="${tool.name} on ${on_string}: Matrix" />
+        <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} on ${on_string}: Matrix" />
         <expand macro="output_graphic_outputs" />
         <expand macro="output_save_matrix_values" />
     </outputs>
@@ -242,7 +242,7 @@
             <param name="missingDataAsZero" value="True" />
             <param name="beforeRegionStartLength" value="10" />
             <param name="afterRegionStartLength" value="10" />
-            <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_matrix" compare="sim_size" />
+            <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
         </test>
         <test>
             <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
@@ -252,7 +252,7 @@
             <param name="binSize" value="10" />
             <param name="beforeRegionStartLength" value="10" />
             <param name="afterRegionStartLength" value="10" />
-            <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_matrix" compare="sim_size" />
+            <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
         </test>
     </tests>
   <help>