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comparison temp.xml @ 1:39cbc0965e07 draft

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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
author portiahollyoak
date Mon, 25 Apr 2016 13:15:41 -0400
parents 28d1a6f8143f
children 7ac983da5ad8
comparison
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0:28d1a6f8143f 1:39cbc0965e07
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}.bai" && 15 ln -f -s "$alignment.metadata.bam_index" "$alignment.element_identifier".bam.bai &&
16 ln -f -s "${alignment}" "${alignment.element_identifier}.bam" && 16 ln -f -s "$alignment" "$alignment.element_identifier".bam &&
17 bash $__tool_directory__/scripts/TEMP_Insertion.sh -i "$alignment" -s $__tool_directory__/scripts -r "$consensus_te_seqs" -t "$bed_te_locations" -m 3 -f "$median_insertsize" -c \${GALAXY_SLOTS:-2} && 17 bash $__tool_directory__/scripts/TEMP_Insertion.sh -i "$alignment.element_identifier".bam -s $__tool_directory__/scripts -r "$consensus_te_seqs" -t "$bed_te_locations" -m 3 -f "$median_insertsize" -c \${GALAXY_SLOTS:-2} &&
18 bash $__tool_directory__/scripts/TEMP_Absence.sh -i "$alignment" -s $__tool_directory__/scripts -r "$bed_te_locations" -t "$reference2bit" -f 500 -c \${GALAXY_SLOTS:-2} && 18 bash $__tool_directory__/scripts/TEMP_Absence.sh -i "$alignment.element_identifier".bam -s $__tool_directory__/scripts -r "$bed_te_locations" -t "$reference2bit" -f 500 -c \${GALAXY_SLOTS:-2} &&
19 mv ${alignment.element_identifier}.insertion.bp.bed $insertion_bed && 19 mv "$alignment.element_identifier".insertion.bp.bed $insertion_bed &&
20 mv ${alignment.element_identifier}.insertion.refined.bp $insertion_bed_refined && 20 mv "$alignment.element_identifier".insertion.refined.bp $insertion_bed_refined &&
21 mv ${alignment.element_identifier}.insertion.refined.bp.summary $insertion_summary && 21 mv "$alignment.element_identifier".insertion.refined.bp.summary $insertion_summary &&
22 mv ${alignment.element_identifier}.absence.refined.bp.summary $absence_summary && 22 mv "$alignment.element_identifier".absence.refined.bp.summary $absence_summary &&
23 zip $archive *insertion* *excision* *absence* 23 zip $archive *insertion* *excision* *absence*
24 ]]></command> 24 ]]></command>
25 <inputs> 25 <inputs>
26 <param format="bam" name="alignment" type="data" label="Alignment bam file"/> 26 <param format="bam" name="alignment" type="data" label="Alignment bam file"/>
27 <param format="twobit" name="reference2bit" type="data" label="Reference twobit file"/> 27 <param format="twobit" name="reference2bit" type="data" label="Reference twobit file"/>