Mercurial > repos > iuc > bedtools
comparison multiCov.xml @ 11:7308cc546a36 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
author | iuc |
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date | Mon, 17 Oct 2016 10:13:35 -0400 |
parents | c78cf6fe3018 |
children | 95a3b2c25bd1 |
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10:c78cf6fe3018 | 11:7308cc546a36 |
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11 ln -s -f $bam ${i}.bam && | 11 ln -s -f $bam ${i}.bam && |
12 ln -s -f $bam.metadata.bam_index ${i}.bam.bai && | 12 ln -s -f $bam.metadata.bam_index ${i}.bam.bai && |
13 #end for | 13 #end for |
14 | 14 |
15 bedtools multicov | 15 bedtools multicov |
16 -bed $input | 16 -bed '$input' |
17 -bams | 17 -bams |
18 #for $i, $bam in enumerate( $bams ): | 18 #for $i, $bam in enumerate( $bams ): |
19 ${i}.bam | 19 '${i}.bam' |
20 #end for | 20 #end for |
21 $strand | 21 $strand |
22 -f $overlap | 22 -f $overlap |
23 $reciprocal | 23 $reciprocal |
24 $split | 24 $split |
25 -q $q | 25 -q $q |
26 $duplicate | 26 $duplicate |
27 $failed | 27 $failed |
28 $proper | 28 $proper |
29 > $output | 29 > '$output' |
30 ]]> | 30 ]]> |
31 </command> | 31 </command> |
32 <inputs> | 32 <inputs> |
33 <param name="input" format="bed" type="data" label="Sorted BED file" /> | 33 <param name="input" format="bed" type="data" label="Sorted BED file" /> |
34 <!-- Additional files, if the user needs more --> | 34 <!-- Additional files, if the user needs more --> |
41 <param name="q" type="integer" value="0" label="Minimum mapping quality (MAPQ) allowed" help="(-q)" /> | 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="" | 42 <param name="duplicate" type="boolean" checked="False" truevalue="-D" falsevalue="" |
43 label="Include duplicate reads" | 43 label="Include duplicate reads" |
44 help="Default counts non-duplicates only. (-D)" /> | 44 help="Default counts non-duplicates only. (-D)" /> |
45 <param name="failed" type="boolean" checked="false" truevalue="-F" falsevalue="" | 45 <param name="failed" type="boolean" checked="false" truevalue="-F" falsevalue="" |
46 label="Include failed-QC reads" | 46 label="Include failed-QC reads" |
47 help="Default counts pass-QC reads only (-F)"/> | 47 help="Default counts pass-QC reads only (-F)"/> |
48 <param name="proper" type="boolean" checked="false" truevalue="-p" falsevalue="" | 48 <param name="proper" type="boolean" checked="false" truevalue="-p" falsevalue="" |
49 label="Only count proper pairs" | 49 label="Only count proper pairs" |
50 help="Default counts all alignments with MAPQ > -q argument, regardless of the BAM FLAG field. (-p)" /> | 50 help="Default counts all alignments with MAPQ > -q argument, regardless of the BAM FLAG field. (-p)" /> |
51 </inputs> | 51 </inputs> |