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comparison temp.xml @ 8:f60f60cf4a34 draft

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planemo upload for repository https://github.com/portiahollyoak/Tools commit 2bc118a40da59fc3a2b8ee9ed04152c8effff94f
author portiahollyoak
date Tue, 26 Apr 2016 06:27:41 -0400
parents e96a0d0f8dd6
children 20a6e46295d6
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7:e96a0d0f8dd6 8:f60f60cf4a34
1 <tool id ="run_TEMP" name="Run TEMP" version=" 0.1.0"> 1 <tool id ="run_TEMP" name="Run TEMP" version=" 0.1.1">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.1.19">samtools</requirement> 4 <requirement type="package" version="0.1.19">samtools</requirement>
5 <requirement type="package" version="1.6.924">perl-bioperl</requirement> 5 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
6 <requirement type="package" version="0.7.13">bwa</requirement> 6 <requirement type="package" version="0.7.13">bwa</requirement>
10 <stdio> 10 <stdio>
11 <exit_code range="1:" /> 11 <exit_code range="1:" />
12 </stdio> 12 </stdio>
13 <command><![CDATA[ 13 <command><![CDATA[
14 14
15 ln -f -s "$alignment.metadata.bam_index" "$alignment.element_identifier".sorted.bam.bai && 15 ln -f -s "$alignment.metadata.bam_index" alignment.sorted.bam.bai &&
16 ln -f -s "$alignment" "$alignment.element_identifier".sorted.bam && 16 ln -f -s "$alignment" alignment.sorted.bam &&
17 ls -l ; 17 bash $__tool_directory__/scripts/TEMP_Insertion.sh -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$consensus_te_seqs" -t "$bed_te_locations" -m 3 -f "$median_insertsize" -c \${GALAXY_SLOTS:-2} && ls -l &&
18 bash $__tool_directory__/scripts/TEMP_Insertion.sh -i "$alignment.element_identifier".sorted.bam -s $__tool_directory__/scripts -r "$consensus_te_seqs" -t "$bed_te_locations" -m 3 -f "$median_insertsize" -c \${GALAXY_SLOTS:-2} && ls -l && 18 bash $__tool_directory__/scripts/TEMP_Absence.sh -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$bed_te_locations" -t "$reference2bit" -f 500 -c \${GALAXY_SLOTS:-2} &&
19 bash $__tool_directory__/scripts/TEMP_Absence.sh -i "$alignment.element_identifier".sorted.bam -s $__tool_directory__/scripts -r "$bed_te_locations" -t "$reference2bit" -f 500 -c \${GALAXY_SLOTS:-2} && 19 mv alignment.insertion.bp.bed $insertion_bed &&
20 mv "$alignment.element_identifier".insertion.bp.bed $insertion_bed && 20 mv alignment.insertion.refined.bp $insertion_bed_refined &&
21 mv "$alignment.element_identifier".insertion.refined.bp $insertion_bed_refined && 21 mv alignment.insertion.refined.bp.summary $insertion_summary &&
22 mv "$alignment.element_identifier".insertion.refined.bp.summary $insertion_summary && 22 mv alignment.absence.refined.bp.summary $absence_summary &&
23 mv "$alignment.element_identifier".absence.refined.bp.summary $absence_summary &&
24 zip archive.zip *insertion* *excision* *absence* && 23 zip archive.zip *insertion* *excision* *absence* &&
25 mv archive.zip $archive 24 mv archive.zip $archive
26 ]]></command> 25 ]]></command>
27 <inputs> 26 <inputs>
28 <param format="bam" name="alignment" type="data" label="Alignment bam file"/> 27 <param format="bam" name="alignment" type="data" label="Alignment bam file"/>