Mercurial > repos > portiahollyoak > temp
comparison temp.xml @ 3:7c1d80867e88 draft
planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
author | portiahollyoak |
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date | Mon, 25 Apr 2016 14:08:06 -0400 |
parents | 7ac983da5ad8 |
children | 8c8cc2e2c0bc |
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2:7ac983da5ad8 | 3:7c1d80867e88 |
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1 <tool id ="run_TEMP" name="Run TEMP" version=" 0.1.0"> | 1 <tool id ="run_TEMP" name="Run TEMP" version=" 0.1.0"> |
2 <description></description> | 2 <description></description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="0.1.19">samtools</requirement> | |
4 <requirement type="package" version="1.6.924">perl-bioperl</requirement> | 5 <requirement type="package" version="1.6.924">perl-bioperl</requirement> |
5 <requirement type="package" version="0.7.13">bwa</requirement> | 6 <requirement type="package" version="0.7.13">bwa</requirement> |
6 <requirement type="package" version="2.25.0">bedtools</requirement> | 7 <requirement type="package" version="2.25.0">bedtools</requirement> |
7 <requirement type="package" version="0.1.19">samtools</requirement> | |
8 <requirement type="package" version="324">ucsc-twobittofa</requirement> | 8 <requirement type="package" version="324">ucsc-twobittofa</requirement> |
9 </requirements> | 9 </requirements> |
10 <stdio> | 10 <stdio> |
11 <exit_code range="1:" /> | 11 <exit_code range="1:" /> |
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 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} && | 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 && |
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".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 && |