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comparison temp.xml @ 4:8c8cc2e2c0bc draft

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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
author portiahollyoak
date Mon, 25 Apr 2016 14:13:34 -0400
parents 7c1d80867e88
children 2d566f713aec
comparison
equal deleted inserted replaced
3:7c1d80867e88 4:8c8cc2e2c0bc
13 <command><![CDATA[ 13 <command><![CDATA[
14 14
15 ln -f -s "$alignment.metadata.bam_index" "$alignment.element_identifier".bam.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 ls -l ; 17 ls -l ;
18 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} && 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 &&
19 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 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 *insertion* *excision* *absence*