Mercurial > repos > bgruening > hicexplorer_hicbuildmatrix

comparison hicBuildMatrix.xml @ 6:30d427846764 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 8def073a083b0619e366436a067a614555190058
author iuc
date Tue, 02 Jan 2018 10:14:52 -0500
parents 3bc1425f9000
children be42758f532e
comparison
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5:3bc1425f9000 6:30d427846764
1 <tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.1">
2 <description>creates a contact matrix</description> 2 <description>creates a contact matrix</description>
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>
59 --QCfolder ./QCfolder 59 --QCfolder ./QCfolder
60 && 60 &&
61 mv ./QCfolder/* $qc.files_path/ 61 mv ./QCfolder/* $qc.files_path/
62 && 62 &&
63 mv $qc.files_path/hicQC.html $qc 63 mv $qc.files_path/hicQC.html $qc
64 && mv $qc.files_path/*.log raw_qc
64 && samtools sort ./unsorted.bam -o sorted.bam 65 && samtools sort ./unsorted.bam -o sorted.bam
65 66
66 ]]> 67 ]]>
67 </command> 68 </command>
68 <inputs> 69 <inputs>
126 </data> 127 </data>
127 <data name="outFileName_cool" from_work_dir="matrix.cool" format="cool" label="${tool.name} MATRIX on ${on_string}"> 128 <data name="outFileName_cool" from_work_dir="matrix.cool" format="cool" label="${tool.name} MATRIX on ${on_string}">
128 <filter>outputFormat == 'cool'</filter> 129 <filter>outputFormat == 'cool'</filter>
129 </data> 130 </data>
130 <data name="qc" format="html" label="${tool.name} QC"/> 131 <data name="qc" format="html" label="${tool.name} QC"/>
132 <data name="raw_qc" from_work_dir='raw_qc' label="${tool.name} raw QC" />
131 </outputs> 133 </outputs>
132 <tests> 134 <tests>
133 <test> 135 <test>
134 <repeat name="samFiles"> 136 <repeat name="samFiles">
135 <param name="samFile" value="small_test_R1_unsorted.sam"/> 137 <param name="samFile" value="small_test_R1_unsorted.sam"/>
143 </conditional> 145 </conditional>
144 <param name='outputFormat' value='h5'/> 146 <param name='outputFormat' value='h5'/>
145 147
146 <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/> 148 <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/>
147 <output name="outFileName_h5" file="small_test_matrix_2.h5" ftype="h5" compare="sim_size"/> 149 <output name="outFileName_h5" file="small_test_matrix_2.h5" ftype="h5" compare="sim_size"/>
150 <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/>
148 </test> 151 </test>
149 </tests> 152 </tests>
150 <help><![CDATA[ 153 <help><![CDATA[
151 154
152 Creation of the contact matrix 155 Creation of the contact matrix