Mercurial > repos > iuc > bam_to_scidx

comparison bam_to_scidx.xml @ 2:bd79c4d39af0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit d12fc0b2960551d8659d7079e15a3d4e214786b3
author iuc
date Wed, 15 Jun 2016 10:50:24 -0400
parents ebbf2a6a4c55
children 11fc60f0e942
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1:ebbf2a6a4c55 2:bd79c4d39af0
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> 3 <requirements>
4 <requirement type="package" version="8.0.45">java-jdk</requirement> 4 <requirement type="package" version="8.0.45">java-jdk</requirement>
5 </requirements> 5 </requirements>
6 <stdio>
7 <!-- Anything other than zero is an error -->
8 <exit_code range=":-1" />
9 <exit_code range="1:" />
10 <!-- Check stderr in case the return code has not been set -->
11 <regex match="Error:" />
12 <regex match="Exception:" />
13 </stdio>
6 <command> 14 <command>
7 <![CDATA[ 15 <![CDATA[
8 ln -f -s "${input_bam.metadata.bam_index}" "${input_bam}.bai" && 16 ln -f -s "${input_bam.metadata.bam_index}" "${input_bam}.bai" &&
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 17 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
10 ]]> 18 ]]>