Mercurial > repos > devteam > picard
comparison picard_CollectWgsMetrics.xml @ 9:41b8d087a2d2 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
author | devteam |
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date | Wed, 07 Dec 2016 14:56:16 -0500 |
parents | e417b1d6288d |
children | 486d7500da69 |
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8:e417b1d6288d | 9:41b8d087a2d2 |
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17 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) | 17 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) |
18 #end if | 18 #end if |
19 | 19 |
20 picard | 20 picard |
21 CollectWgsMetrics | 21 CollectWgsMetrics |
22 INPUT='$inputFile.element_identifier' | 22 INPUT='$escaped_element_identifier' |
23 OUTPUT="${outFile}" | 23 OUTPUT="${outFile}" |
24 REFERENCE_SEQUENCE="${reference_fasta_filename}" | 24 REFERENCE_SEQUENCE="${reference_fasta_filename}" |
25 MINIMUM_MAPPING_QUALITY="${minimum_mapping_quality}" | 25 MINIMUM_MAPPING_QUALITY="${minimum_mapping_quality}" |
26 MINIMUM_BASE_QUALITY="${minimum_base_quality}" | 26 MINIMUM_BASE_QUALITY="${minimum_base_quality}" |
27 COVERAGE_CAP="${coverage_cap}" | 27 COVERAGE_CAP="${coverage_cap}" |