Mercurial > repos > iuc > bam_to_scidx

comparison bam_to_scidx.xml @ 1:ebbf2a6a4c55 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit f33b04533bca91242b8a0a4077e1d593f5a874e0
author iuc
date Tue, 19 Apr 2016 18:10:09 -0400
parents 741b8af6386c
children bd79c4d39af0
comparison
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0:741b8af6386c 1:ebbf2a6a4c55
1 <tool id="bam_to_scidx" name="Convert BAM to ScIdx" version="1.0.0"> 1 <tool id="bam_to_scidx" name="Convert BAM to ScIdx" version="1.0.0">
2 <description></description> 2 <description></description>
3 <requirements>
4 <requirement type="package" version="8.0.45">java-jdk</requirement>
5 </requirements>
3 <command> 6 <command>
4 <![CDATA[ 7 <![CDATA[
5 ln -f -s "${input_bam.metadata.bam_index}" "${input_bam}.bai" && 8 ln -f -s "${input_bam.metadata.bam_index}" "${input_bam}.bai" &&
6 java -jar $__tool_directory__/BAMtoscIDX.jar -b "$input_bam" -i "${input_bam}.bai" -p $require_proper_mate_pairing -r $read -m $min_insert_size -M $max_insert_size -o "$output" 1>/dev/null 9 java -jar $__tool_directory__/BAMtoscIDX.jar -b "$input_bam" -i "${input_bam}.bai" -p $require_proper_mate_pairing -r $read -m $min_insert_size -M $max_insert_size -o "$output" 1>/dev/null
7 ]]> 10 ]]>
26 <tests> 29 <tests>
27 <test> 30 <test>
28 <param name="input_bam" value="input.bam" ftype="bam" /> 31 <param name="input_bam" value="input.bam" ftype="bam" />
29 <param name="require_proper_mate_pairing" value="1" /> 32 <param name="require_proper_mate_pairing" value="1" />
30 <param name="read" value="0" /> 33 <param name="read" value="0" />
31 <output name="output" file="output.scidx" lines_diff="1" ftype="scidx" /> 34 <output name="output" file="output.scidx" lines_diff="1" ftype="scidx" compare="contains" />
32 </test> 35 </test>
33 </tests> 36 </tests>
34 <help> 37 <help>
35 38
36 **What it does** 39 **What it does**