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comparison samtools_bedcov.xml @ 2:12749212f61b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_bedcov commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:17:25 -0400
parents 8c3472790020
children 9149ad20699a
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1:8c3472790020 2:12749212f61b
1 <tool id="samtools_bedcov" name="BedCov" version="2.0"> 1 <tool id="samtools_bedcov" name="BedCov" version="2.0.1">
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"></expand> 6 <expand macro="requirements"/>
7 <expand macro="stdio"></expand> 7 <expand macro="stdio"/>
8 <expand macro="version_command"></expand> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 for bamfile in 10 ## Ensure simlinks have unique filenames
11 #for dataset in $input_bams: 11 #for $i, $bam in enumerate( $input_bams ):
12 "${dataset}" 12 ln -s -f '${bam}' '${i}.bam' &&
13 ln -s -f '${bam.metadata.bam_index}' '${i}.bam.bai' &&
13 #end for 14 #end for
14 ; do 15
15 if [ ! -f \$bamfile.bai ] ; then 16 samtools bedcov
16 ln -s \$bamfile && samtools index `basename \$bamfile` ; 17 '${input_bed}'
17 else 18 #for $i in range(len( $input_bams )):
18 ln -s \$bamfile && ln -s \$bamfile.bai ; 19 '${i}.bam'
19 fi ; 20 #end for
20 done ; 21 > '${output}'
21 samtools bedcov "${input_bed}" 22 ]]></command>
22 #for dataset in $input_bams:
23 `basename "${dataset}"`
24 #end for
25 > "${output}"
26 ]]>
27 </command>
28 <inputs> 23 <inputs>
29 <param name="input_bed" type="data" format="bed" label="BED file" /> 24 <param name="input_bed" type="data" format="bed" label="Genemic intervals (in BED format)" />
30 <param name="input_bams" type="data" format="bam" label="BAM file" multiple="true" /> 25 <param name="input_bams" type="data" format="bam" multiple="true" label="BAM file(s)" />
31 </inputs> 26 </inputs>
32 <outputs> 27 <outputs>
33 <data format="tabular" name="output" label="${tool.name} on ${on_string}" /> 28 <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
34 </outputs> 29 </outputs>
35 <tests> 30 <tests>
36 <test> 31 <test>
37 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" /> 32 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
38 <param name="input_bams" value="eboVir3.bam" ftype="bam" /> 33 <param name="input_bams" value="eboVir3.bam" ftype="bam" />
48 **What it does** 43 **What it does**
49 44
50 Calculates read depth for regions listed in a BED dataset using ``samtools bedcov`` command:: 45 Calculates read depth for regions listed in a BED dataset using ``samtools bedcov`` command::
51 46
52 samtools bedcov [INPUT BED] [INPUT BAM1] ... [INPUT BAMn] > [OUTPUT] 47 samtools bedcov [INPUT BED] [INPUT BAM1] ... [INPUT BAMn] > [OUTPUT]
53
54 </help> 48 </help>
55 <expand macro="citations"></expand> 49 <expand macro="citations"/>
56 </tool> 50 </tool>
57