Mercurial > repos > portiahollyoak > temp
comparison temp.xml @ 10:3200a0299230 draft
planemo upload for repository https://github.com/portiahollyoak/Tools commit debe4684eaa00ffcae3c79e7581fdbe41da91d5d
author | portiahollyoak |
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date | Wed, 27 Apr 2016 11:44:13 -0400 |
parents | 20a6e46295d6 |
children | e19d9742c99b |
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9:20a6e46295d6 | 10:3200a0299230 |
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1 <tool id ="run_TEMP" name="Run TEMP" version=" 0.1.1"> | 1 <tool id ="run_TEMP" name="Run TEMP" version=" 0.1.2"> |
2 <description></description> | 2 <description></description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="0.1.19">samtools</requirement> | 4 <!-- The following are classical toolshed packages and should be removed |
5 once conda is deemed stable--> | |
6 <requirement type="package" version="1.6.922">bioperl</requirement> | |
7 <requirement type="package" version="0.7.12">bwa</requirement> | |
8 <requirement type="package" version="2.24">bedtools</requirement> | |
9 <!-- end of toolshed package definitions --> | |
5 <requirement type="package" version="1.6.924">perl-bioperl</requirement> | 10 <requirement type="package" version="1.6.924">perl-bioperl</requirement> |
6 <requirement type="package" version="0.7.13">bwa</requirement> | 11 <requirement type="package" version="0.7.13">bwa</requirement> |
7 <requirement type="package" version="2.25.0">bedtools</requirement> | 12 <requirement type="package" version="2.25.0">bedtools</requirement> |
8 <requirement type="package" version="324">ucsc-twobittofa</requirement> | 13 <requirement type="package" version="324">ucsc-twobittofa</requirement> |
14 <requirement type="package" version="0.1.19">samtools</requirement> | |
9 </requirements> | 15 </requirements> |
10 <stdio> | 16 <stdio> |
11 <exit_code range="1:" /> | 17 <exit_code range="1:" /> |
12 </stdio> | 18 </stdio> |
13 <command><![CDATA[ | 19 <command><![CDATA[ |
14 | 20 |
15 ln -f -s "$alignment.metadata.bam_index" alignment.sorted.bam.bai && | 21 ln -f -s "$alignment.metadata.bam_index" alignment.sorted.bam.bai && |
16 ln -f -s "$alignment" alignment.sorted.bam && | 22 ln -f -s "$alignment" alignment.sorted.bam && |
17 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 && | 23 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} && |
18 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} && | 24 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} && |
19 mv alignment.insertion.bp.bed $insertion_bed && | 25 mv alignment.insertion.bp.bed $insertion_bed && |
20 mv alignment.insertion.refined.bp $insertion_bed_refined && | 26 mv alignment.insertion.refined.bp $insertion_bed_refined && |
21 mv alignment.insertion.refined.bp.summary $insertion_summary && | 27 mv alignment.insertion.refined.bp.summary $insertion_summary && |
22 mv alignment.absence.refined.bp.summary $absence_summary && | 28 mv alignment.absence.refined.bp.summary $absence_summary && |