Mercurial > repos > iuc > schicexplorer_schicqualitycontrol

comparison scHicQualityControl.xml @ 2:f623007a57d1 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d
author iuc
date Fri, 14 Apr 2023 14:09:31 +0000
parents e06c31798a26
children
comparison
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1:e06c31798a26 2:f623007a57d1
1 <tool id="schicexplorer_schicqualitycontrol" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="schicexplorer_schicqualitycontrol" name="@BINARY@" version="@TOOL_VERSION@.1" profile="@PROFILE@">
2 <description>quality control for single-cell Hi-C interaction matrices</description> 2 <description>quality control for single-cell Hi-C interaction matrices</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">scHicQualityControl</token> 4 <token name="@BINARY@">scHicQualityControl</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 ## https://github.com/open2c/cooler/issues/299
10 cp '$matrix_scooler' matrix.scooler &&
11
9 @BINARY@ 12 @BINARY@
10 13
11 --matrix '$matrix_scooler' 14 --matrix matrix.scooler
12 #if $chromosomes: 15 #if $chromosomes:
13 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ]) 16 #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
14 --chromosomes $chromosome 17 --chromosomes $chromosome
15 #end if 18 #end if
16 --minimumReadCoverage $minimumReadCoverage 19 --minimumReadCoverage $minimumReadCoverage