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comparison macs2_refinepeak.xml @ 2:bfe57d6e0c4c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
author iuc
date Mon, 12 Oct 2015 11:24:39 -0400
parents fe62ba547975
children beb902da6e5f
comparison
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1:859c982b1f7f 2:bfe57d6e0c4c
1 <tool id="macs2_refinepeak" name="MACS2 refinepeak" version="@VERSION_STRING@.0"> 1 <tool id="macs2_refinepeak" name="MACS2 refinepeak" version="@VERSION_STRING@.0">
2 <description>Refine peak summits and give scores measuring balance of forward- backward tags (Experimental)</description> 2 <description>Refine peak summits and give scores measuring balance of forward- backward tags (Experimental)</description>
3 <expand macro="requirements" />
4 <expand macro="version_command" />
5 <macros> 3 <macros>
6 <import>macs2_macros.xml</import> 4 <import>macs2_macros.xml</import>
7 </macros> 5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <expand macro="version_command" />
8 <command> 9 <command>
9 macs2 refinepeak 10 macs2 refinepeak
10 -b "${ bed_infile }" 11 -b "${ bed_infile }"
11 -i "${ infile }" 12 -i "${ infile }"
12 --format '${ infile.extension.upper() }' 13 --format '${ infile.extension.upper() }'
13 --cutoff "${ cutoff }" 14 --cutoff "${ cutoff }"
14 --window-size "${ winsize }" 15 --window-size "${ winsize }"
15 --ofile "${ outfile }" 16 --ofile "${ outfile }"
16 </command> 17 </command>
17 <expand macro="stdio" />
18 <inputs> 18 <inputs>
19 <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" /> 19 <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
20 <param name="bed_infile" type="data" format="bed" label="Candidate peak file in BED format" /> 20 <param name="bed_infile" type="data" format="bed" label="Candidate peak file in BED format" />
21 <param name="cutoff" type="float" label="Cutoff" value="5.0" help="default: 5.0 (--cutoff)"/> 21 <param name="cutoff" type="float" label="Cutoff" value="5.0" help="default: 5.0 (--cutoff)"/>
22 <param name="winsize" type="integer" value="200" label="Scan window size on both side of the summit" help="default: 200bp (--window-size)" /> 22 <param name="winsize" type="integer" value="200" label="Scan window size on both side of the summit" help="default: 200bp (--window-size)" />