Mercurial > repos > devteam > picard
diff picard_CollectWgsMetrics.xml @ 8:e417b1d6288d draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
author | devteam |
---|---|
date | Tue, 06 Dec 2016 10:04:26 -0500 |
parents | 08f69add4d06 |
children | 41b8d087a2d2 |
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--- a/picard_CollectWgsMetrics.xml Sun Nov 27 15:11:36 2016 -0500 +++ b/picard_CollectWgsMetrics.xml Tue Dec 06 10:04:26 2016 -0500 @@ -6,29 +6,30 @@ <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @java_options@ + @symlink_element_identifier@ ##set up input files #set $reference_fasta_filename = "localref.fa" - + #if str( $reference_source.reference_source_selector ) == "history": ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && #else: #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) #end if - + picard CollectWgsMetrics - INPUT="${inputFile}" + INPUT='$inputFile.element_identifier' OUTPUT="${outFile}" REFERENCE_SEQUENCE="${reference_fasta_filename}" MINIMUM_MAPPING_QUALITY="${minimum_mapping_quality}" MINIMUM_BASE_QUALITY="${minimum_base_quality}" COVERAGE_CAP="${coverage_cap}" - + VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - + ]]></command> <inputs> <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> @@ -52,15 +53,15 @@ <param name="minimum_base_quality" type="integer" value="20" label="Minimum base quality for a base to contribute coverage" help="MINIMUM_BASE_QUALITY; default=20"/> <param name="coverage_cap" type="integer" value="250" label="Treat bases with coverage exceeding this value as if they had coverage at this value" help="COVERAGE_CAP; default=250"/> - + <expand macro="VS" /> - + </inputs> - + <outputs> <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/> </outputs> - + <tests> <test> <param name="reference_source_selector" value="history" /> @@ -70,10 +71,10 @@ <param name="ref_file" value="picard_CollectWgsMetrics_ref.fa" /> <param name="inputFile" value="picard_CollectWgsMetrics.bam" ftype="bam" /> <output name="outFile" file="picard_CollectWgsMetrics_test1.tab" ftype="tabular" lines_diff="4"/> - </test> + </test> </tests> - - + + <help> .. class:: infomark @@ -87,14 +88,14 @@ @description@ MINIMUM_MAPPING_QUALITY=Integer - MQ=Integer Minimum mapping quality for a read to contribute coverage. Default value: 20. + MQ=Integer Minimum mapping quality for a read to contribute coverage. Default value: 20. MINIMUM_BASE_QUALITY=Integer - Q=Integer Minimum base quality for a base to contribute coverage. Default value: 20. + Q=Integer Minimum base quality for a base to contribute coverage. Default value: 20. COVERAGE_CAP=Integer - CAP=Integer Treat bases with coverage exceeding this value as if they had coverage at this value. - Default value: 250. + CAP=Integer Treat bases with coverage exceeding this value as if they had coverage at this value. + Default value: 250. @more_info@