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view picard_CollectWgsMetrics.xml @ 5:2f3cdd537834 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 6e148b31fed1b322ce720804d8525088ec6d43f9
author | devteam |
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date | Thu, 29 Oct 2015 22:23:28 -0400 |
parents | 52fdfc45590a |
children | 08f69add4d06 |
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<tool name="CollectWgsMetrics" id="picard_CollectWgsMetrics" version="@TOOL_VERSION@.0"> <description>compute metrics for evaluating of whole genome sequencing experiments</description> <macros> <import>picard_macros.xml</import> </macros> <expand macro="requirements" /> <command> @java_options@ ##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( $reference_source.ref_file.fields.path ) #end if java -jar \$JAVA_JAR_PATH/picard.jar CollectWgsMetrics INPUT="${inputFile}" 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"/> <conditional name="reference_source"> <param name="reference_source_selector" type="select" label="Load reference genome from"> <option value="cached">Local cache</option> <option value="history">History</option> </param> <when value="cached"> <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> <options from_data_table="all_fasta"> </options> <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> </param> </when> <when value="history"> <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> </when> </conditional> <param name="minimum_mapping_quality" type="integer" value="20" label="Minimum mapping quality for a read to contribute coverage" help="MINIMUM_MAPPING_QUALITY; default=20"/> <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" /> <param name="minimum_mapping_quality" value="20" /> <param name="minimum_base_quality" value="20" /> <param name="coverage_cap" value="250" /> <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> </tests> <stdio> <exit_code range="1:" level="fatal"/> </stdio> <help> .. class:: infomark **Purpose** Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments. @dataset_collections@ @description@ MINIMUM_MAPPING_QUALITY=Integer 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. COVERAGE_CAP=Integer CAP=Integer Treat bases with coverage exceeding this value as if they had coverage at this value. Default value: 250. @more_info@ </help> </tool>