Mercurial > repos > iuc > bam_to_scidx

comparison bam_to_scidx.xml @ 5:408520e1ae1a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx commit cadf726e05de4dfc4f2cf708674fcd2828e4c319
author iuc
date Mon, 03 Jul 2017 10:09:42 -0400
parents b737f6d83f48
children
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4:b737f6d83f48 5:408520e1ae1a
1 <tool id="bam_to_scidx" name="Convert BAM to ScIdx" version="1.0.1"> 1 <tool id="bam_to_scidx" name="Convert BAM to ScIdx" version="1.0.1">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="8.0.112">openjdk</requirement> 4 <requirement type="package" version="8.0.112">openjdk</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <command detect_errors="exit_code"><![CDATA[
7 <!-- Anything other than zero is an error --> 7 ln -s '${input_bam}' localbam.bam &&
8 <exit_code range=":-1" /> 8 ln -f -s '${input_bam.metadata.bam_index}' localbam.bam.bai &&
9 <exit_code range="1:" /> 9 java -jar '$__tool_directory__/BAMtoscIDX.jar'
10 <!-- Check stderr in case the return code has not been set --> 10 -b localbam.bam
11 <regex match="Error:" /> 11 -i localbam.bam.bai
12 <regex match="Exception:" /> 12 -p $require_proper_mate_pairing
13 </stdio> 13 -r $read
14 <command> 14 #if str($min_insert_size):
15 <![CDATA[ 15 -m $min_insert_size
16 ln -s "${input_bam}" "localbam.bam" && 16 #end if
17 ln -f -s "${input_bam.metadata.bam_index}" "localbam.bam.bai" && 17 #if str($max_insert_size):
18 java -jar $__tool_directory__/BAMtoscIDX.jar -b localbam.bam -i localbam.bam.bai -p $require_proper_mate_pairing -r $read -m $min_insert_size -M $max_insert_size -o "$output" 1>/dev/null 18 -M $max_insert_size
19 ]]> 19 #end if
20 </command> 20 -o '$output'
21 1>/dev/null
22 ]]></command>
21 <inputs> 23 <inputs>
22 <param name="input_bam" type="data" format="bam" label="BAM file" /> 24 <param name="input_bam" type="data" format="bam" label="BAM file" />
23 <param name="require_proper_mate_pairing" type="select" label="Require proper mate-pairing?" help="Required if filtering by insert size for single-end Reqd 1 (below)." > 25 <param name="require_proper_mate_pairing" type="select" label="Require proper mate-pairing?" help="Required if filtering by insert size for single-end Reqd 1 (below)." >
24 <option value="1" selected="True">Yes</option> 26 <option value="1" selected="True">Yes</option>
25 <option value="0">No</option> 27 <option value="0">No</option>