Mercurial > repos > iuc > bedtools
annotate multiCov.xml @ 25:e36671a0f646 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ee522a02a3fab980a5b32a1387182c951ab04968
author | iuc |
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date | Fri, 20 Apr 2018 05:30:23 -0400 |
parents | 7308cc546a36 |
children | 95a3b2c25bd1 |
rev | line source |
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0 | 1 <tool id="bedtools_multicovtbed" name="MultiCovBed" version="@WRAPPER_VERSION@.0"> |
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607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
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1
diff
changeset
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2 <description>counts coverage from multiple BAMs at specific intervals</description> |
0 | 3 <macros> |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <expand macro="stdio" /> | |
8 <command> | |
1 | 9 <![CDATA[ |
10 #for $i, $bam in enumerate( $bams ): | |
11 ln -s -f $bam ${i}.bam && | |
12 ln -s -f $bam.metadata.bam_index ${i}.bam.bai && | |
0 | 13 #end for |
1 | 14 |
15 bedtools multicov | |
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
10
diff
changeset
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16 -bed '$input' |
1 | 17 -bams |
18 #for $i, $bam in enumerate( $bams ): | |
11
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
10
diff
changeset
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19 '${i}.bam' |
1 | 20 #end for |
21 $strand | |
22 -f $overlap | |
23 $reciprocal | |
24 $split | |
25 -q $q | |
26 $duplicate | |
27 $failed | |
28 $proper | |
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
10
diff
changeset
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29 > '$output' |
1 | 30 ]]> |
0 | 31 </command> |
32 <inputs> | |
1 | 33 <param name="input" format="bed" type="data" label="Sorted BED file" /> |
0 | 34 <!-- Additional files, if the user needs more --> |
1 | 35 <param name="bams" format="bam" type="data" multiple="True" label="BAM file" /> |
36 | |
0 | 37 <expand macro="strand2" /> |
38 <expand macro="overlap" /> | |
1 | 39 <expand macro="reciprocal" /> |
0 | 40 <expand macro="split" /> |
1 | 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="" | |
11
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
10
diff
changeset
|
46 label="Include failed-QC reads" |
1 | 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)" /> | |
0 | 51 </inputs> |
52 <outputs> | |
1 | 53 <data name="output" metadata_source="input" format_source="input" /> |
0 | 54 </outputs> |
1 | 55 <tests> |
56 <test> | |
57 <param name="input" value="multiCov1.bed" ftype="bed" /> | |
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c78cf6fe3018
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6
iuc
parents:
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diff
changeset
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58 <param name="bams" value="srma_in3.bam,srma_in3.bam" ftype="bam"/> |
1 | 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> | |
0 | 64 <help> |
1 | 65 <![CDATA[ |
0 | 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@ | |
1 | 72 ]]> |
0 | 73 </help> |
74 <expand macro="citations" /> | |
75 </tool> |