Mercurial > repos > portiahollyoak > temp
changeset 3:7c1d80867e88 draft
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
| author | portiahollyoak |
|---|---|
| date | Mon, 25 Apr 2016 14:08:06 -0400 |
| parents | 7ac983da5ad8 |
| children | 8c8cc2e2c0bc |
| files | temp.xml |
| diffstat | 1 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/temp.xml Mon Apr 25 13:24:46 2016 -0400 +++ b/temp.xml Mon Apr 25 14:08:06 2016 -0400 @@ -1,10 +1,10 @@ <tool id ="run_TEMP" name="Run TEMP" version=" 0.1.0"> <description></description> <requirements> + <requirement type="package" version="0.1.19">samtools</requirement> <requirement type="package" version="1.6.924">perl-bioperl</requirement> <requirement type="package" version="0.7.13">bwa</requirement> <requirement type="package" version="2.25.0">bedtools</requirement> - <requirement type="package" version="0.1.19">samtools</requirement> <requirement type="package" version="324">ucsc-twobittofa</requirement> </requirements> <stdio> @@ -14,8 +14,8 @@ ln -f -s "$alignment.metadata.bam_index" "$alignment.element_identifier".bam.bai && ln -f -s "$alignment" "$alignment.element_identifier".bam && - samtools ; - 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 ; + 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 && 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 &&