Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

diff hicBuildMatrix.xml @ 12:8bf84c4cb1cb draft

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"planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 91a0182476a7fc26be7bef1677790518c4e88348-dirty"
author bgruening
date Mon, 16 Dec 2019 10:33:21 -0500
parents 495ae38f6e0d
children 4b85ea34afae
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line diff
--- a/hicBuildMatrix.xml	Sat Jun 09 15:35:48 2018 -0400
+++ b/hicBuildMatrix.xml	Mon Dec 16 10:33:21 2019 -0500
@@ -5,7 +5,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" >
-        <requirement type="package" version="1.6">samtools</requirement>
+        <requirement type="package" version="1.9">samtools</requirement>
     </expand>
     <command detect_errors="exit_code"><![CDATA[
 
@@ -63,7 +63,7 @@
         && mv $qc.files_path/*.log raw_qc
         && mv matrix.$outputFormat matrix
         #if $outBam_Boolean:
-            && samtools sort ./unsorted.bam -o sorted.bam
+            && samtools sort -T "\${TMPDIR:-.}" ./unsorted.bam -o sorted.bam
         #end if
 
 ]]>
@@ -163,7 +163,7 @@
             <param name='outputFormat' value='h5'/>
             <param name='outBam_Boolean' value="True" />
             <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/>
-            <output name="outFileName" 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" delta="50000"/>
             <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/>
         </test>
     </tests>