Mercurial > repos > portiahollyoak > temp
changeset 8:f60f60cf4a34 draft
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 |
| files | temp.xml |
| diffstat | 1 files changed, 9 insertions(+), 10 deletions(-) [+] |
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--- a/temp.xml Mon Apr 25 14:20:48 2016 -0400 +++ b/temp.xml Tue Apr 26 06:27:41 2016 -0400 @@ -1,4 +1,4 @@ -<tool id ="run_TEMP" name="Run TEMP" version=" 0.1.0"> +<tool id ="run_TEMP" name="Run TEMP" version=" 0.1.1"> <description></description> <requirements> <requirement type="package" version="0.1.19">samtools</requirement> @@ -12,15 +12,14 @@ </stdio> <command><![CDATA[ - ln -f -s "$alignment.metadata.bam_index" "$alignment.element_identifier".sorted.bam.bai && - ln -f -s "$alignment" "$alignment.element_identifier".sorted.bam && - ls -l ; - 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 && - bash $__tool_directory__/scripts/TEMP_Absence.sh -i "$alignment.element_identifier".sorted.bam -s $__tool_directory__/scripts -r "$bed_te_locations" -t "$reference2bit" -f 500 -c \${GALAXY_SLOTS:-2} && - mv "$alignment.element_identifier".insertion.bp.bed $insertion_bed && - mv "$alignment.element_identifier".insertion.refined.bp $insertion_bed_refined && - mv "$alignment.element_identifier".insertion.refined.bp.summary $insertion_summary && - mv "$alignment.element_identifier".absence.refined.bp.summary $absence_summary && + ln -f -s "$alignment.metadata.bam_index" alignment.sorted.bam.bai && + ln -f -s "$alignment" alignment.sorted.bam && + 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 && + 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} && + mv alignment.insertion.bp.bed $insertion_bed && + mv alignment.insertion.refined.bp $insertion_bed_refined && + mv alignment.insertion.refined.bp.summary $insertion_summary && + mv alignment.absence.refined.bp.summary $absence_summary && zip archive.zip *insertion* *excision* *absence* && mv archive.zip $archive ]]></command>