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comparison multiCov.xml @ 26:c0fbce5dc84a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
author iuc
date Mon, 17 Oct 2016 10:13:20 -0400
parents a2d4c30ba2f9
children d279800f4ff9
comparison
equal deleted inserted replaced
25:6c6963cf9136 26:c0fbce5dc84a
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>
53 <data name="output" metadata_source="input" format_source="input" /> 53 <data name="output" metadata_source="input" format_source="input" />
54 </outputs> 54 </outputs>
55 <tests> 55 <tests>
56 <test> 56 <test>
57 <param name="input" value="multiCov1.bed" ftype="bed" /> 57 <param name="input" value="multiCov1.bed" ftype="bed" />
58 <param name="bams" value="srma_in3.bam,srma_in3.bam" ftpye="bam"/> 58 <param name="bams" value="srma_in3.bam,srma_in3.bam" ftype="bam"/>
59 <param name="q" value="1"/> 59 <param name="q" value="1"/>
60 <param name="split" value="False"/> 60 <param name="split" value="False"/>
61 <output name="output" file="multiCovBed_result1.bed" ftype="bed" /> 61 <output name="output" file="multiCovBed_result1.bed" ftype="bed" />
62 </test> 62 </test>
63 </tests> 63 </tests>