Mercurial > repos > bgruening > hicexplorer_hicplotdistvscounts

diff hicPlotDistVsCounts.xml @ 10:d7a84a789c83 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2307743fd10f0babde52eec30289fe1682236287
author iuc
date Sat, 09 Jun 2018 15:34:40 -0400
parents c886ddb8e122
children 34dc1acfcc62
line wrap: on
line diff
--- a/hicPlotDistVsCounts.xml	Fri Apr 27 08:39:05 2018 -0400
+++ b/hicPlotDistVsCounts.xml	Sat Jun 09 15:34:40 2018 -0400
@@ -30,6 +30,10 @@
             #if $chromosomeExclude:
                 --chromosomeExclude '$chroms'
             #end if
+
+            #if $outFileData_Boolean:
+                $outFileData_Boolean ./outFileData
+            #end if
 ]]>
     </command>
     <inputs>
@@ -49,9 +53,14 @@
                 <validator type="empty_field" />
             </param>
         </repeat>
+        <param name='outFileData_Boolean' type='boolean' truevalue='--outFileData'  falsevalue="" checked="false" label="Save data underlying the plots as BAM"
+            help="A bam file containing all data underlying the plots is saved on this file."/>
     </inputs>
     <outputs>
         <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on [${on_string}]: Plot"/>
+        <data name="outFileData" from_work_dir="outFileData" format="txt" label="${tool.name} data file on ${on_string}">
+            <filter>outFileData_Boolean</filter>
+        </data>
     </outputs>
     <tests>
         <test>
@@ -60,6 +69,13 @@
             <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/>
         </test>
         <test>
+            <param name="matrices" ftype="h5" value="small_test_matrix_50kb_res.h5"/>
+            <param name="skipDiagonal" value="False"/>
+            <param name='outFileData_Boolean' value='True'/>
+            <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/>
+            <output name="outFileData" file="distVsCounts.txt" ftype="txt" compare="sim_size" delta='600'/>
+        </test>
+        <test>
             <param name="matrices" ftype="h5" value="small_test_matrix_50kb_res.h5,small_test_matrix_50kb_res.h5"/>
             <param name="skipDiagonal" value="False"/>
             <param name="perchr" value="True" />