Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

comparison 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
comparison
equal deleted inserted replaced
11:4ceaee0043a5 12:8bf84c4cb1cb
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicBuildMatrix</token> 4 <token name="@BINARY@">hicBuildMatrix</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" > 7 <expand macro="requirements" >
8 <requirement type="package" version="1.6">samtools</requirement> 8 <requirement type="package" version="1.9">samtools</requirement>
9 </expand> 9 </expand>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 11
12 mkdir ./QCfolder && 12 mkdir ./QCfolder &&
13 mkdir $qc.files_path && 13 mkdir $qc.files_path &&
61 && 61 &&
62 mv $qc.files_path/hicQC.html $qc 62 mv $qc.files_path/hicQC.html $qc
63 && mv $qc.files_path/*.log raw_qc 63 && mv $qc.files_path/*.log raw_qc
64 && mv matrix.$outputFormat matrix 64 && mv matrix.$outputFormat matrix
65 #if $outBam_Boolean: 65 #if $outBam_Boolean:
66 && samtools sort ./unsorted.bam -o sorted.bam 66 && samtools sort -T "\${TMPDIR:-.}" ./unsorted.bam -o sorted.bam
67 #end if 67 #end if
68 68
69 ]]> 69 ]]>
70 </command> 70 </command>
71 <inputs> 71 <inputs>
161 <param name="binSize" value="5000"/> 161 <param name="binSize" value="5000"/>
162 </conditional> 162 </conditional>
163 <param name='outputFormat' value='h5'/> 163 <param name='outputFormat' value='h5'/>
164 <param name='outBam_Boolean' value="True" /> 164 <param name='outBam_Boolean' value="True" />
165 <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/> 165 <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/>
166 <output name="outFileName" file="small_test_matrix_2.h5" ftype="h5" compare="sim_size"/> 166 <output name="outFileName" file="small_test_matrix_2.h5" ftype="h5" compare="sim_size" delta="50000"/>
167 <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/> 167 <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/>
168 </test> 168 </test>
169 </tests> 169 </tests>
170 <help><![CDATA[ 170 <help><![CDATA[
171 171