Mercurial > repos > iuc > macs2
annotate macs2_bdgbroadcall.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_bdgbroadcall" name="MACS2 bdgbroadcall" version="@VERSION_STRING@.0"> |
| 2 <description>Call broad peaks from bedGraph output</description> | |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
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3 <macros> |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
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4 <import>macs2_macros.xml</import> |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
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5 </macros> |
| 0 | 6 <expand macro="requirements"> |
| 7 <requirement type="package" version="4.1.0">gnu_awk</requirement> | |
| 8 </expand> | |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
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0
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changeset
|
9 <expand macro="stdio" /> |
| 0 | 10 <expand macro="version_command" /> |
| 11 <command> | |
| 12 macs2 bdgbroadcall | |
| 13 --ifile "${ infile }" | |
| 14 --cutoff-peak "${ cutoffpeak }" | |
| 15 --cutoff-link "${ cutofflink }" | |
| 16 --min-length "${ minlen }" | |
| 17 --lvl1-max-gap "${ LVL1MAXGAP }" | |
| 18 --lvl2-max-gap "${ LVL2MAXGAP }" | |
| 19 --ofile "macs2_bdgbroadcall.bdg" | |
| 20 && | |
| 21 awk '!/^track name/' "macs2_bdgbroadcall.bdg" > "${ outfile }" | |
| 22 </command> | |
| 23 <inputs> | |
| 24 <param name="infile" type="data" format="bedgraph" label="MACS score in bedGraph" /> | |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
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25 <param name="cutoffpeak" type="float" label="Cutoff for peaks" value="2.0" |
| 0 | 26 help="Cutoff for peaks depending on which method you used for score track. If the file contains qvalue scores from MACS2, score 2 means qvalue 0.01. default: 2.0 (--cutoff-peak)"/> |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
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0
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changeset
|
27 <param name="cutofflink" type="float" label="Cutoff for peaks" value="1.0" |
| 0 | 28 help=" Cutoff for linking regions/low abundance regions depending on which method you used for score track. If the file contains qvalue scores from MACS2, score 1 means qvalue 0.1, and score 0.3 means qvalue 0.5. default: 1 (--cutoff-link)"/> |
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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
|
29 <param name="minlen" type="integer" label="Minimum length of peak" value="200" |
| 0 | 30 help="It is recommended to set it as d value." /> |
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2
bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents:
0
diff
changeset
|
31 <param name="LVL1MAXGAP" type="integer" label="Maximum gap between significant peaks" value="30" |
| 0 | 32 help="It is recommended to set it to tag size" /> |
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2
bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents:
0
diff
changeset
|
33 <param name="LVL2MAXGAP" type="integer" label="Maximum linking between significant peaks" value="800" |
| 0 | 34 help="It is recommended to set it to 4 times of d value" /> |
| 35 </inputs> | |
| 36 <outputs> | |
| 37 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" /> | |
| 38 </outputs> | |
| 39 <tests> | |
| 40 <test> | |
| 41 <param name="infile" value="callpeak_treatment_part.bdg" ftype="bedgraph" /> | |
| 42 <param name="cutoffpeak" value="2.0"/> | |
| 43 <param name="cutofflink" value="1.0"/> | |
| 44 <param name="minlen" value="200"/> | |
| 45 <param name="LVL1MAXGAP" value="30"/> | |
| 46 <param name="LVL2MAXGAP" value="800"/> | |
| 47 <output name="outfile" file="bdgbroadcall_on_callpeak_treatment.tabular"/> | |
| 48 </test> | |
| 49 </tests> | |
| 50 <help> | |
| 51 **What it does** | |
| 52 | |
| 53 Call broad peaks from bedGraph output. | |
| 54 bdgbroadcall from macs2 | |
| 55 | |
| 56 @citation@ | |
| 57 </help> | |
| 58 <expand macro="citations" /> | |
| 59 </tool> |