Mercurial > repos > devteam > picard
comparison picard_CollectRnaSeqMetrics.xml @ 15:a5a13ea16d17 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
author | iuc |
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date | Tue, 19 Jun 2018 11:28:30 -0400 |
parents | 486d7500da69 |
children | 2474cd44d10a |
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14:486d7500da69 | 15:a5a13ea16d17 |
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1 <tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> | 1 <tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> |
2 <description> collect metrics about the alignment of RNA to various functional classes of loci in the genome</description> | 2 <description> collect metrics about the alignment of RNA to various functional classes of loci in the genome</description> |
3 <macros> | 3 <macros> |
4 <import>picard_macros.xml</import> | 4 <import>picard_macros.xml</import> |
5 <token name="@WRAPPER_VERSION@">0</token> | 5 <token name="@WRAPPER_VERSION@">1</token> |
6 </macros> | 6 </macros> |
7 <expand macro="requirements"> | 7 <expand macro="requirements"> |
8 <requirement type="package" version="3.4.1">r-base</requirement> | 8 <requirement type="package" version="3.4.1">r-base</requirement> |
9 <requirement type="package" version="357">ucsc-gff3togenepred</requirement> | 9 <requirement type="package" version="357">ucsc-gff3togenepred</requirement> |
10 <requirement type="package" version="357">ucsc-gtftogenepred</requirement> | 10 <requirement type="package" version="357">ucsc-gtftogenepred</requirement> |
57 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}" | 57 METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}" |
58 INPUT='$escaped_element_identifier' | 58 INPUT='$escaped_element_identifier' |
59 OUTPUT="${outFile}" | 59 OUTPUT="${outFile}" |
60 REFERENCE_SEQUENCE="${reference_fasta_filename}" | 60 REFERENCE_SEQUENCE="${reference_fasta_filename}" |
61 ASSUME_SORTED="${assume_sorted}" | 61 ASSUME_SORTED="${assume_sorted}" |
62 | 62 @TMPDIR_OPTION@ |
63 VALIDATION_STRINGENCY=${validation_stringency} | 63 VALIDATION_STRINGENCY=${validation_stringency} |
64 | 64 |
65 ]]></command> | 65 ]]></command> |
66 | 66 |
67 <inputs> | 67 <inputs> |