Mercurial > repos > iuc > macs2
comparison macs2_refinepeak.xml @ 0:fe62ba547975 draft
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| author | iuc |
|---|---|
| date | Wed, 11 Feb 2015 10:18:02 -0500 |
| parents | |
| children | bfe57d6e0c4c |
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| -1:000000000000 | 0:fe62ba547975 |
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| 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> | |
| 3 <expand macro="requirements" /> | |
| 4 <expand macro="version_command" /> | |
| 5 <macros> | |
| 6 <import>macs2_macros.xml</import> | |
| 7 </macros> | |
| 8 <command> | |
| 9 macs2 refinepeak | |
| 10 -b "${ bed_infile }" | |
| 11 -i "${ infile }" | |
| 12 --format '${ infile.extension.upper() }' | |
| 13 --cutoff "${ cutoff }" | |
| 14 --window-size "${ winsize }" | |
| 15 --ofile "${ outfile }" | |
| 16 </command> | |
| 17 <expand macro="stdio" /> | |
| 18 <inputs> | |
| 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" /> | |
| 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)" /> | |
| 23 </inputs> | |
| 24 | |
| 25 <outputs> | |
| 26 <data name="outfile" format="bed" label="${tool.name} on ${on_string}" /> | |
| 27 </outputs> | |
| 28 <tests> | |
| 29 <test> | |
| 30 <param name="infile" value="ChIP_200K.bed" ftype="bed"/> | |
| 31 <param name="bed_infile" value="callpeak_summits_part.bed" ftype="bed"/> | |
| 32 <param name="cutoff" value="5.0"/> | |
| 33 <param name="winsize" value="200"/> | |
| 34 <output name="outfile" file="refinepeak_ChIP_and_summits.bed"/> | |
| 35 </test> | |
| 36 </tests> | |
| 37 <help> | |
| 38 **What it does** | |
| 39 | |
| 40 (Experimental) Take raw reads alignment, refine peak summits and give scores measuring balance of forward- backward tags. Inspired by SPP. | |
| 41 | |
| 42 @citation@ | |
| 43 </help> | |
| 44 <expand macro="citations" /> | |
| 45 </tool> |