Mercurial > repos > portiahollyoak > temp
diff temp.xml @ 1:39cbc0965e07 draft
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 |
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--- a/temp.xml Mon Apr 25 13:08:56 2016 -0400 +++ b/temp.xml Mon Apr 25 13:15:41 2016 -0400 @@ -12,14 +12,14 @@ </stdio> <command><![CDATA[ - ln -f -s "${alignment.metadata.bam_index}" "${alignment.element_identifier}.bai" && - ln -f -s "${alignment}" "${alignment.element_identifier}.bam" && - 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} && - 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} && - 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" "$alignment.element_identifier".bam.bai && + ln -f -s "$alignment" "$alignment.element_identifier".bam && + 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} && + bash $__tool_directory__/scripts/TEMP_Absence.sh -i "$alignment.element_identifier".bam -s $__tool_directory__/scripts -r "$bed_te_locations" -t "$reference2bit" -f 500 -c \${GALAXY_SLOTS:-2} && + mv "$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 && zip $archive *insertion* *excision* *absence* ]]></command> <inputs>