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comparison macs2_bdgpeakcall.xml @ 9:acbd3fb47f90 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
author iuc
date Thu, 25 Jan 2018 02:11:52 -0500
parents beb902da6e5f
children 640d3af5d833
comparison
equal deleted inserted replaced
8:e8a060164e11 9:acbd3fb47f90
4 <import>macs2_macros.xml</import> 4 <import>macs2_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <expand macro="version_command" /> 8 <expand macro="version_command" />
9 <command> 9 <command><![CDATA[
10 <![CDATA[ 10 @home_dir@
11
12 macs2 bdgpeakcall 11 macs2 bdgpeakcall
13 --ifile '${ infile }' 12 --ifile '${ infile }'
14 --cutoff '${ cutoff }' 13 --cutoff '${ cutoff }'
15 --min-length '${ minlen }' 14 --min-length '${ minlen }'
16 --max-gap '${ maxgap }' 15 --max-gap '${ maxgap }'
17 ${ cutoff_analysis } 16 ${ cutoff_analysis }
18 ${ notrackline } 17 ${ notrackline }
19 --ofile '${ outfile }' 18 --ofile '${ outfile }'
20 19 ]]></command>
21 ]]>
22 </command>
23 <inputs> 20 <inputs>
24 <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" /> 21 <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" />
25 <param name="cutoff" type="float" label="Cutoff for peaks" value="5.0" 22 <param name="cutoff" type="float" label="Cutoff for peaks" value="5.0"
26 help="Cutoff depends on which method you used for score track. If the file contains pvalue scores from MACS2, score 5 means pvalue 1e-5. Default=5.0 (--cutoff)"/> 23 help="Cutoff depends on which method you used for score track. If the file contains pvalue scores from MACS2, score 5 means pvalue 1e-5. Default=5.0 (--cutoff)"/>
27 <param name="minlen" type="integer" value="200" label="Minimum length of peak" help="better to set it as d value. Default=200 (--min-length)"/> 24 <param name="minlen" type="integer" value="200" label="Minimum length of peak" help="better to set it as d value. Default=200 (--min-length)"/>