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picard: implement missing parameters #4737

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Aug 22, 2022
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picard: implement missing parameters #4737

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5 changes: 3 additions & 2 deletions tools/picard/picard_CollectSequencingArtifactsMetrics.xml
View file
Original file line number Diff line number Diff line change
@@ -2,7 +2,7 @@
<description>Collect metrics to quantify single-base sequencing artifacts</description>
<macros>
<import>picard_macros.xml</import>
<token name="@WRAPPER_VERSION@">1</token>
<token name="@WRAPPER_VERSION@">2</token>
</macros>
<expand macro="requirements">
<requirement type="package" version="3.4.1">r-base</requirement>
@@ -31,7 +31,8 @@
INCLUDE_UNPAIRED='${unpaired}'
MAXIMUM_INSERT_SIZE='${max_size}'
MINIMUM_INSERT_SIZE='${min_size}'
MINIMUM_MAPPING_QUALITY='${minim_map_quality}';
MINIMUM_MAPPING_QUALITY='${minim_map_quality}'
VALIDATION_STRINGENCY='${validation_stringency}';
]]></command>
<inputs>
<param name='inputFile' format="sam,bam" type='data' label='SAM/BAM Input file'/>
3 changes: 2 additions & 1 deletion tools/picard/picard_ValidateSamFile.xml
View file
Original file line number Diff line number Diff line change
@@ -2,7 +2,7 @@
<description>assess validity of SAM/BAM dataset</description>
<macros>
<import>picard_macros.xml</import>
<token name="@WRAPPER_VERSION@">1</token>
<token name="@WRAPPER_VERSION@">2</token>
</macros>
<expand macro="requirements" />
<stdio>
@@ -45,6 +45,7 @@
REFERENCE_SEQUENCE="${reference_fasta_filename}"
IGNORE_WARNINGS="${ignore_warnings}"
IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}"
VALIDATE_INDEX="${validate_index}"
MAX_OPEN_TEMP_FILES=`ulimit -Sn`
VERBOSITY=ERROR