Mercurial > repos > portiahollyoak > temp

comparison temp.xml @ 3:7c1d80867e88 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
2:7ac983da5ad8 3:7c1d80867e88
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 &&