Mercurial > repos > iuc > bedtools
annotate multiCov.xml @ 35:ac2040a5e6ff draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
| author | iuc |
|---|---|
| date | Fri, 08 Dec 2017 03:26:23 -0500 |
| parents | c0fbce5dc84a |
| children | d279800f4ff9 |
| rev | line source |
|---|---|
| 8 | 1 <tool id="bedtools_multicovtbed" name="MultiCovBed" version="@WRAPPER_VERSION@.0"> |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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changeset
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2 <description>counts coverage from multiple BAMs at specific intervals</description> |
| 8 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 #for $i, $bam in enumerate( $bams ): | |
| 11 ln -s -f $bam ${i}.bam && | |
| 12 ln -s -f $bam.metadata.bam_index ${i}.bam.bai && | |
| 13 #end for | |
| 14 | |
| 15 bedtools multicov | |
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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
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16 -bed '$input' |
| 8 | 17 -bams |
| 18 #for $i, $bam in enumerate( $bams ): | |
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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
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19 '${i}.bam' |
| 8 | 20 #end for |
| 21 $strand | |
| 22 -f $overlap | |
| 23 $reciprocal | |
| 24 $split | |
| 25 -q $q | |
| 26 $duplicate | |
| 27 $failed | |
| 28 $proper | |
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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
|
29 > '$output' |
| 8 | 30 ]]> |
| 31 </command> | |
| 32 <inputs> | |
| 33 <param name="input" format="bed" type="data" label="Sorted BED file" /> | |
| 34 <!-- Additional files, if the user needs more --> | |
| 35 <param name="bams" format="bam" type="data" multiple="True" label="BAM file" /> | |
| 36 | |
| 37 <expand macro="strand2" /> | |
| 38 <expand macro="overlap" /> | |
| 39 <expand macro="reciprocal" /> | |
| 40 <expand macro="split" /> | |
| 41 <param name="q" type="integer" value="0" label="Minimum mapping quality (MAPQ) allowed" help="(-q)" /> | |
| 42 <param name="duplicate" type="boolean" checked="False" truevalue="-D" falsevalue="" | |
| 43 label="Include duplicate reads" | |
| 44 help="Default counts non-duplicates only. (-D)" /> | |
| 45 <param name="failed" type="boolean" checked="false" truevalue="-F" falsevalue="" | |
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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
|
46 label="Include failed-QC reads" |
| 8 | 47 help="Default counts pass-QC reads only (-F)"/> |
| 48 <param name="proper" type="boolean" checked="false" truevalue="-p" falsevalue="" | |
| 49 label="Only count proper pairs" | |
| 50 help="Default counts all alignments with MAPQ > -q argument, regardless of the BAM FLAG field. (-p)" /> | |
| 51 </inputs> | |
| 52 <outputs> | |
| 53 <data name="output" metadata_source="input" format_source="input" /> | |
| 54 </outputs> | |
| 55 <tests> | |
| 56 <test> | |
| 57 <param name="input" value="multiCov1.bed" ftype="bed" /> | |
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26
c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
|
58 <param name="bams" value="srma_in3.bam,srma_in3.bam" ftype="bam"/> |
| 8 | 59 <param name="q" value="1"/> |
| 60 <param name="split" value="False"/> | |
| 61 <output name="output" file="multiCovBed_result1.bed" ftype="bed" /> | |
| 62 </test> | |
| 63 </tests> | |
| 64 <help> | |
| 65 <![CDATA[ | |
| 66 **What it does** | |
| 67 | |
| 68 bedtools multicov, reports the count of alignments from multiple position-sorted and indexed BAM files that overlap intervals in a BED file. Specifically, for each BED interval provided, it reports a separate count of overlapping alignments from each BAM file. | |
| 69 | |
| 70 | |
| 71 @REFERENCES@ | |
| 72 ]]> | |
| 73 </help> | |
| 74 <expand macro="citations" /> | |
| 75 </tool> |