changeset 7:be42758f532e draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01

--- a/hicBuildMatrix.xml	Tue Jan 02 10:14:52 2018 -0500
+++ b/hicBuildMatrix.xml	Wed Jan 03 13:28:16 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.1">
+<tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.2">
     <description>creates a contact matrix</description>
     <macros>
         <token name="@BINARY@">hicBuildMatrix</token>
@@ -37,11 +37,8 @@
                 --region '$region'
             #end if
 
-            #if $outputFormat == 'h5'
-                --outFileName matrix.h5
-            #elif $outputFormat == 'cool'
-                --outFileName matrix.cool
-            #end if
+            --outFileName matrix.$outputFormat
+        
             --outBam ./unsorted.bam
 
             $keepSelfCircles
@@ -62,6 +59,7 @@
         &&
         mv $qc.files_path/hicQC.html $qc
         && mv $qc.files_path/*.log raw_qc
+        && mv matrix.$outputFormat matrix
         && samtools sort ./unsorted.bam -o sorted.bam
        
 ]]>
@@ -122,14 +120,14 @@
     </inputs>
     <outputs>
         <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/>
-        <data name="outFileName_h5" from_work_dir="matrix.h5" format="h5" label="${tool.name} MATRIX on ${on_string}">
-            <filter>outputFormat == 'h5'</filter>
-        </data>
-        <data name="outFileName_cool" from_work_dir="matrix.cool" format="cool" label="${tool.name} MATRIX on ${on_string}">
-            <filter>outputFormat == 'cool'</filter>
+        <data name="outFileName" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}">
+            <change_format>
+                <when input="outputFormat" value="cool" format="cool" />
+            </change_format>
         </data>
         <data name="qc" format="html" label="${tool.name} QC"/>
-        <data name="raw_qc" from_work_dir='raw_qc' label="${tool.name} raw QC" />
+
+        <data name="raw_qc" from_work_dir='raw_qc' format='txt' label="${tool.name} raw QC" />
     </outputs>
     <tests>
         <test>
@@ -146,7 +144,7 @@
             <param name='outputFormat' value='h5'/>
 
             <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/>
-            <output name="outFileName_h5" file="small_test_matrix_2.h5" ftype="h5" compare="sim_size"/>
+            <output name="outFileName" file="small_test_matrix_2.h5" ftype="h5" compare="sim_size"/>
             <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/>
         </test>
     </tests>
@@ -212,7 +210,7 @@
 Read orientation:
 _________________
 - inward pairs
-- outward pairs
+- outward pairs 
 - left pairs
 - right pairs