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comparison temp.xml @ 2:7ac983da5ad8 draft

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planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
author portiahollyoak
date Mon, 25 Apr 2016 13:24:46 -0400
parents 39cbc0965e07
children 7c1d80867e88
comparison
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1:39cbc0965e07 2:7ac983da5ad8
12 </stdio> 12 </stdio>
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 samtools ;
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 $__tool_directory__/scripts/TEMP_Insertion.sh -i "$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.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".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 $insertion_bed && 20 mv "$alignment.element_identifier".insertion.bp.bed $insertion_bed &&
20 mv "$alignment.element_identifier".insertion.refined.bp $insertion_bed_refined && 21 mv "$alignment.element_identifier".insertion.refined.bp $insertion_bed_refined &&
21 mv "$alignment.element_identifier".insertion.refined.bp.summary $insertion_summary && 22 mv "$alignment.element_identifier".insertion.refined.bp.summary $insertion_summary &&