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comparison temp.xml @ 19:e541089245ba draft

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planemo upload for repository https://github.com/portiahollyoak/Tools commit 264ceb3f8eae0938d6c97d0e01985cd9ce511467
author mvdbeek
date Thu, 01 Sep 2016 11:11:59 -0400
parents e198b686bfe4
children 6e02b9179a24
comparison
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18:e198b686bfe4 19:e541089245ba
1 <tool id ="run_TEMP" name="TEMP" version="0.2.1"> 1 <tool id ="run_TEMP" name="TEMP" version="0.2.2">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <!-- The following are classical toolshed packages and should be removed 4 <!-- The following are classical toolshed packages and should be removed
5 once conda is deemed stable--> 5 once conda is deemed stable-->
6 <requirement type="package" version="1.6.922">bioperl</requirement> 6 <requirement type="package" version="1.6.922">bioperl</requirement>
39 -t "$reference2bit" 39 -t "$reference2bit"
40 -f "$median_insertsize" 40 -f "$median_insertsize"
41 -c \${GALAXY_SLOTS:-2} && 41 -c \${GALAXY_SLOTS:-2} &&
42 mv alignment.insertion.refined.bp.summary $insertion_summary && 42 mv alignment.insertion.refined.bp.summary $insertion_summary &&
43 mv alignment.absence.refined.bp.summary $absence_summary && 43 mv alignment.absence.refined.bp.summary $absence_summary &&
44 tar -czf archive.tar.gz *insertion* *excision* *absence* && mv archive.tar.gz $archive 44 tar -czf archive.tar.gz *insertion* *excision* && mv archive.tar.gz $archive
45 ]]></command> 45 ]]></command>
46 <inputs> 46 <inputs>
47 <param format="bam" name="alignment" type="data" label="Alignment bam file"/> 47 <param format="bam" name="alignment" type="data" label="Alignment bam file"/>
48 <param format="twobit" name="reference2bit" type="data" label="Reference twobit file"/> 48 <param format="twobit" name="reference2bit" type="data" label="Reference twobit file"/>
49 <param format="fasta" name="consensus_te_seqs" type="data" label="Consensus TE Seqs fasta file"/> 49 <param format="fasta" name="consensus_te_seqs" type="data" label="Consensus TE Seqs fasta file"/>