Mercurial > repos > iuc > macs2
annotate macs2_bdgpeakcall.xml @ 42:8f48c6ac8293 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 48fbe322d0f3ec023186989104ae4f4188b03a1d
| author | iuc |
|---|---|
| date | Mon, 01 Jun 2015 22:48:32 -0400 |
| parents | 8c8ae1e19b10 |
| children | 1b3f899ef044 |
| rev | line source |
|---|---|
| 33 | 1 <tool id="macs2_bdgpeakcall" name="MACS2 bdgpeakcall" version="@VERSION_STRING@.0"> |
| 2 <description>Call peaks from bedGraph output</description> | |
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8c8ae1e19b10
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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33
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changeset
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3 <macros> |
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8c8ae1e19b10
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
33
diff
changeset
|
4 <import>macs2_macros.xml</import> |
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8c8ae1e19b10
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
33
diff
changeset
|
5 </macros> |
| 33 | 6 <expand macro="requirements"> |
| 7 <requirement type="package" version="4.1.0">gnu_awk</requirement> | |
| 8 </expand> | |
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36
8c8ae1e19b10
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
33
diff
changeset
|
9 <expand macro="stdio" /> |
| 33 | 10 <expand macro="version_command" /> |
| 11 <command> | |
| 12 macs2 bdgpeakcall | |
| 13 --ifile "${ infile }" | |
| 14 --cutoff "${ cutoff }" | |
| 15 --min-length "${ minlen }" | |
| 16 --max-gap "${ maxgap }" | |
| 17 ${ callsummits } | |
| 18 ${ notrackline } | |
| 19 --ofile "macs2_bdgpeakcall.bdg" | |
| 20 && | |
| 21 awk '!/^track name/' "macs2_bdgpeakcall.bdg" > "${ outfile }" | |
| 22 </command> | |
| 23 <inputs> | |
| 24 <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" /> | |
| 25 | |
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36
8c8ae1e19b10
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
33
diff
changeset
|
26 <param name="cutoff" type="float" label="Cutoff for peaks" value="5.0" |
| 33 | 27 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)"/> |
| 28 <param name="minlen" type="integer" value="200" label="Minimum length of peak" help="better to set it as d value (--min-length)"/> | |
| 29 <param name="maxgap" type="integer" value="30" label="Maximum gap between significant points in a peak" help="better to set it as tag size DEFAULT: 30 (--max-gap)"/> | |
| 30 | |
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36
8c8ae1e19b10
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
33
diff
changeset
|
31 <param name="callsummits" type="boolean" truevalue="--call-summits" falsevalue="" checked="False" |
| 33 | 32 label="If set, MACS will use a more sophisticated approach to find all summits in each enriched peak region." |
| 33 help="(-call-summits)"/> | |
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36
8c8ae1e19b10
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
33
diff
changeset
|
34 <param name="notrackline" type="boolean" truevalue="" falsevalue="--no-trackline" checked="False" |
| 33 | 35 label="Include trackline into bedGraph output" |
| 36 help="required by USCS (--no-trackline)"/> | |
| 37 </inputs> | |
| 38 <outputs> | |
| 39 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" /> | |
| 40 </outputs> | |
| 41 <tests> | |
| 42 <test> | |
| 43 <param name="infile" value="callpeak_treatment_part.bdg" ftype="bedgraph" /> | |
| 44 <param name="cutoff" value="5.0"/> | |
| 45 <param name="minlen" value="200"/> | |
| 46 <param name="maxgap" value="30"/> | |
| 47 <output name="outfile" file="bdgpeakcall_on_callpeak_treatment.tabular"/> | |
| 48 </test> | |
| 49 </tests> | |
| 50 <help> | |
| 51 **What it does** | |
| 52 | |
| 53 Call peaks from bedGraph output. | |
| 54 bdgpeakcall from macs2 | |
| 55 | |
| 56 | |
| 57 @citation@ | |
| 58 </help> | |
| 59 <expand macro="citations" /> | |
| 60 </tool> |