Mercurial > repos > iuc > macs2
annotate macs2_refinepeak.xml @ 2:bfe57d6e0c4c draft
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 |
| rev | line source |
|---|---|
| 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> | |
| 3 <macros> | |
| 4 <import>macs2_macros.xml</import> | |
| 5 </macros> | |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents:
0
diff
changeset
|
6 <expand macro="requirements" /> |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents:
0
diff
changeset
|
7 <expand macro="stdio" /> |
|
bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents:
0
diff
changeset
|
8 <expand macro="version_command" /> |
| 0 | 9 <command> |
| 10 macs2 refinepeak | |
| 11 -b "${ bed_infile }" | |
| 12 -i "${ infile }" | |
| 13 --format '${ infile.extension.upper() }' | |
| 14 --cutoff "${ cutoff }" | |
| 15 --window-size "${ winsize }" | |
| 16 --ofile "${ outfile }" | |
| 17 </command> | |
| 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> |