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comparison macs2_refinepeak.xml @ 5:beb902da6e5f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
author iuc
date Sat, 08 Apr 2017 08:28:57 -0400
parents bfe57d6e0c4c
children acbd3fb47f90
comparison
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4:56e104999978 5:beb902da6e5f
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>
10 <![CDATA[
10 macs2 refinepeak 11 macs2 refinepeak
11 -b "${ bed_infile }" 12 -b '${ bed_infile }'
12 -i "${ infile }" 13 -i '${ infile }'
13 --format '${ infile.extension.upper() }' 14 --format '${ infile.extension.upper() }'
14 --cutoff "${ cutoff }" 15 --cutoff '${ cutoff }'
15 --window-size "${ winsize }" 16 --window-size '${ winsize }'
16 --ofile "${ outfile }" 17 --ofile '${ outfile }'
18 ]]>
17 </command> 19 </command>
18 <inputs> 20 <inputs>
19 <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" /> 21 <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" /> 22 <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)"/> 23 <param name="cutoff" type="float" label="Cutoff" value="5.0" help="default: 5.0 (--cutoff)"/>
25 <outputs> 27 <outputs>
26 <data name="outfile" format="bed" label="${tool.name} on ${on_string}" /> 28 <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
27 </outputs> 29 </outputs>
28 <tests> 30 <tests>
29 <test> 31 <test>
30 <param name="infile" value="ChIP_200K.bed" ftype="bed"/> 32 <param name="infile" value="refinepeak_bam_input.bam" ftype="bam"/>
31 <param name="bed_infile" value="callpeak_summits_part.bed" ftype="bed"/> 33 <param name="bed_infile" value="refinepeak_bed_input.bed" ftype="bed"/>
32 <param name="cutoff" value="5.0"/> 34 <param name="cutoff" value="5.0"/>
33 <param name="winsize" value="200"/> 35 <param name="winsize" value="200"/>
34 <output name="outfile" file="refinepeak_ChIP_and_summits.bed"/> 36 <output name="outfile" file="refinepeak_output.bed"/>
35 </test> 37 </test>
36 </tests> 38 </tests>
37 <help> 39 <help>
40 <![CDATA[
38 **What it does** 41 **What it does**
39 42
40 (Experimental) Take raw reads alignment, refine peak summits and give scores measuring balance of forward- backward tags. Inspired by SPP. 43 This is **refinepeak** utility from the MACS2_ Package. It is an experimental utility that takes raw read alignments, refines peak summits and gives scores measuring balance of forward- backward tags. Inspired by the SPP_ pipeline.
44
45 .. _MACS2: https://github.com/taoliu/MACS
46 .. _SPP: http://compbio.med.harvard.edu/Supplements/ChIP-seq/
41 47
42 @citation@ 48 @citation@
49 ]]>
43 </help> 50 </help>
44 <expand macro="citations" /> 51 <expand macro="citations" />
45 </tool> 52 </tool>