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comparison temp.xml @ 6:50c432ca4d1e draft

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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
author portiahollyoak
date Mon, 25 Apr 2016 14:18:37 -0400
parents 2d566f713aec
children e96a0d0f8dd6
comparison
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5:2d566f713aec 6:50c432ca4d1e
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 bash $__tool_directory__/scripts/TEMP_Absence.sh -i "$alignment.element_identifier".sorted.bam -s $__tool_directory__/scripts -r "$bed_te_locations" -t "$reference2bit" -f 500 -c \${GALAXY_SLOTS:-2} &&
20 mv "$alignment.element_identifier".insertion.bp.bed $insertion_bed && 20 mv "$alignment.element_identifier".insertion.bp.bed $insertion_bed &&
21 mv "$alignment.element_identifier".insertion.refined.bp $insertion_bed_refined && 21 mv "$alignment.element_identifier".insertion.refined.bp $insertion_bed_refined &&
22 mv "$alignment.element_identifier".insertion.refined.bp.summary $insertion_summary && 22 mv "$alignment.element_identifier".insertion.refined.bp.summary $insertion_summary &&
23 mv "$alignment.element_identifier".absence.refined.bp.summary $absence_summary && 23 mv "$alignment.element_identifier".absence.refined.bp.summary $absence_summary &&
24 zip $archive *insertion* *excision* *absence* 24 zip archive.zip *insertion* *excision* *absence* &&
25 mv $archive
25 ]]></command> 26 ]]></command>
26 <inputs> 27 <inputs>
27 <param format="bam" name="alignment" type="data" label="Alignment bam file"/> 28 <param format="bam" name="alignment" type="data" label="Alignment bam file"/>
28 <param format="twobit" name="reference2bit" type="data" label="Reference twobit file"/> 29 <param format="twobit" name="reference2bit" type="data" label="Reference twobit file"/>
29 <param format="fasta" name="consensus_te_seqs" type="data" label="Consensus TE Seqs fasta file"/> 30 <param format="fasta" name="consensus_te_seqs" type="data" label="Consensus TE Seqs fasta file"/>