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comparison samtools_bedcov.xml @ 4:b7ab754899d5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit a972815cbd43dea553b3c0e4ad548f35d0023228-dirty
author iuc
date Sun, 28 Jul 2019 14:46:16 -0400
parents e371922c38e8
children 540155c5abee
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3:e371922c38e8 4:b7ab754899d5
1 <tool id="samtools_bedcov" name="BedCov" version="2.0.1"> 1 <tool id="samtools_bedcov" name="BedCov" version="2.0.2">
2 <description>calculate read depth for a set of genomic intervals</description> 2 <description>calculate read depth for a set of genomic intervals</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 ## Ensure simlinks have unique filenames 10 @PREPARE_IDX_MULTIPLE@
11 #for $i, $bam in enumerate( $input_bams ):
12 ln -s -f '${bam}' '${i}.bam' &&
13 ln -s -f '${bam.metadata.bam_index}' '${i}.bam.bai' &&
14 #end for
15 11
16 samtools bedcov 12 samtools bedcov
13 #if $mapq:
14 -Q $mapq
15 #end if
16 $countdel
17 '${input_bed}' 17 '${input_bed}'
18 #for $i in range(len( $input_bams )): 18 #for $i in range(len( $input_bams )):
19 '${i}.bam' 19 '${i}'
20 #end for 20 #end for
21 > '${output}' 21 > '${output}'
22 ]]></command> 22 ]]></command>
23 <inputs> 23 <inputs>
24 <param name="input_bed" type="data" format="bed" label="Genemic intervals (in BED format)" /> 24 <param name="input_bed" type="data" format="bed" label="Genemic intervals (in BED format)" />
25 <param name="input_bams" type="data" format="bam" multiple="true" label="BAM file(s)" /> 25 <param name="input_bams" type="data" format="bam" multiple="true" label="BAM file(s)" />
26 <param name="mapq" argument="-Q" type="integer" value="" optional="true" label="Minimum MAPQ" help="Only count reads with mapping quality greater than this value" />
27 <param name="countdel" argument="-j" type="boolean" checked="false" truevalue="-j" falsevalue="" label="Exclude deletions and ref skips" help=" Do not include deletions (D) and ref skips (N) in bedcov computation" />
26 </inputs> 28 </inputs>
27 <outputs> 29 <outputs>
28 <data name="output" format="tabular" label="${tool.name} on ${on_string}" /> 30 <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
29 </outputs> 31 </outputs>
30 <tests> 32 <tests>
36 <test> 38 <test>
37 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" /> 39 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
38 <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" /> 40 <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
39 <output name="output" file="samtools_bedcov_out2.tab" /> 41 <output name="output" file="samtools_bedcov_out2.tab" />
40 </test> 42 </test>
43 <test>
44 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
45 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
46 <param name="mapq" value="40"/>
47 <output name="output" file="samtools_bedcov_out1.tab" />
48 </test>
49 <test>
50 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
51 <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" />
52 <param name="countdel" value="-j" />
53 <output name="output" file="samtools_bedcov_out2.tab" />
54 </test>
41 </tests> 55 </tests>
42 <help> 56 <help>
43 **What it does** 57 **What it does**
44 58
45 Calculates read depth for regions listed in a BED dataset using ``samtools bedcov`` command:: 59 Calculates read depth for regions listed in a BED dataset using ``samtools bedcov`` command::