Mercurial > repos > portiahollyoak > temp
comparison temp.xml @ 18:e198b686bfe4 draft
planemo upload for repository https://github.com/portiahollyoak/Tools commit edf843bf10fa262f075980626a9201078f868757
author | mvdbeek |
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date | Wed, 17 Aug 2016 11:49:25 -0400 |
parents | e7d3dc3e0ec9 |
children | e541089245ba |
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17:e7d3dc3e0ec9 | 18:e198b686bfe4 |
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1 <tool id ="run_TEMP" name="TEMP" version="0.2.0"> | 1 <tool id ="run_TEMP" name="TEMP" version="0.2.1"> |
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> |
37 -s $__tool_directory__/scripts | 37 -s $__tool_directory__/scripts |
38 -r "$te_locations" | 38 -r "$te_locations" |
39 -t "$reference2bit" | 39 -t "$reference2bit" |
40 -f "$median_insertsize" | 40 -f "$median_insertsize" |
41 -c \${GALAXY_SLOTS:-2} && | 41 -c \${GALAXY_SLOTS:-2} && |
42 zip archive.zip *insertion* *excision* *absence* && mv archive.zip $archive && | |
43 mv alignment.insertion.refined.bp.summary $insertion_summary && | 42 mv alignment.insertion.refined.bp.summary $insertion_summary && |
44 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 $archive | |
45 ]]></command> | 45 ]]></command> |
46 <inputs> | 46 <inputs> |
47 <param format="bam" name="alignment" type="data" label="Alignment bam file"/> | 47 <param format="bam" name="alignment" type="data" label="Alignment bam file"/> |
48 <param format="twobit" name="reference2bit" type="data" label="Reference twobit file"/> | 48 <param format="twobit" name="reference2bit" type="data" label="Reference twobit file"/> |
49 <param format="fasta" name="consensus_te_seqs" type="data" label="Consensus TE Seqs fasta file"/> | 49 <param format="fasta" name="consensus_te_seqs" type="data" label="Consensus TE Seqs fasta file"/> |
54 <param name="minimum_score_difference" type="integer" min="10" max="37" value="30" label="Minimum difference between mapping scores"/> | 54 <param name="minimum_score_difference" type="integer" min="10" max="37" value="30" label="Minimum difference between mapping scores"/> |
55 </inputs> | 55 </inputs> |
56 <outputs> | 56 <outputs> |
57 <data format="bed" type="data" name="insertion_summary" label="${alignment.element_identifier} Insertions" /> | 57 <data format="bed" type="data" name="insertion_summary" label="${alignment.element_identifier} Insertions" /> |
58 <data format="bed" type="data" name="absence_summary" label="${alignment.element_identifier} Absences" /> | 58 <data format="bed" type="data" name="absence_summary" label="${alignment.element_identifier} Absences" /> |
59 <data format="zip" type="data" name="archive" label="${alignment.element_identifier} Compressed output files" /> | 59 <data format="tar" type="data" name="archive" label="${alignment.element_identifier} Compressed output files" /> |
60 </outputs> | 60 </outputs> |
61 <tests> | 61 <tests> |
62 <test> | 62 <test> |
63 <param name="alignment" value="chr2l_bwa_mem.bam" ftype="bam"/> | 63 <param name="alignment" value="chr2l_bwa_mem.bam" ftype="bam"/> |
64 <param name="reference2bit" value="dm6_chr2l.twobit" ftype="twobit"/> | 64 <param name="reference2bit" value="dm6_chr2l.twobit" ftype="twobit"/> |