Mercurial > repos > iuc > bam_to_scidx

comparison bam_to_scidx.xml @ 3:11fc60f0e942 draft

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author iuc
date Wed, 22 Jun 2016 09:46:19 -0400
parents bd79c4d39af0
children b737f6d83f48
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2:bd79c4d39af0 3:11fc60f0e942
11 <regex match="Error:" /> 11 <regex match="Error:" />
12 <regex match="Exception:" /> 12 <regex match="Exception:" />
13 </stdio> 13 </stdio>
14 <command> 14 <command>
15 <![CDATA[ 15 <![CDATA[
16 ln -f -s "${input_bam.metadata.bam_index}" "${input_bam}.bai" && 16 ln -s "${input_bam}" "localbam.bam" &&
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 17 ln -f -s "${input_bam.metadata.bam_index}" "localbam.bam.bai" &&
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 ]]> 19 ]]>
19 </command> 20 </command>
20 <inputs> 21 <inputs>
21 <param name="input_bam" type="data" format="bam" label="BAM file" /> 22 <param name="input_bam" type="data" format="bam" label="BAM file" />
22 <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)." > 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)." >