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view picard_QualityScoreDistribution.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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<tool name="QualityScoreDistribution" id="picard_QualityScoreDistribution" version="@TOOL_VERSION@.0"> <description>chart quality score distribution</description> <macros> <import>picard_macros.xml</import> </macros> <expand macro="requirements"> <requirement type="package" version="3.3.1">r</requirement> </expand> <command detect_errors="exit_code"><![CDATA[ @java_options@ ##set up input files @symlink_element_identifier@ #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( $reference_source.ref_file.fields.path ) #end if picard QualityScoreDistribution INPUT='$escaped_element_identifier' OUTPUT="${outFile}" CHART_OUTPUT="${pdfFile}" REFERENCE_SEQUENCE="${reference_fasta_filename}" ALIGNED_READS_ONLY="${aligned_reads_only}" PF_READS_ONLY="${pf_reads_only}" INCLUDE_NO_CALLS="${include_no_calls}" ASSUME_SORTED="${assume_sorted}" VALIDATION_STRINGENCY="${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="aligned_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true, calculate mean quality over aligned reads only" help="ALIGNED_READS_ONLY; default=False"/> <param name="pf_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true calculate mean quality over reads passing quality filter" help="PF_READS_ONLY; default=False"/> <param name="include_no_calls" type="boolean" label="If set to true, include quality for no-call bases in the distribution" help="INCLUDE_NO_CALLS; default=False"/> <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED; default=True"/> <expand macro="VS" /> </inputs> <outputs> <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/> <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/> </outputs> <tests> <test> <param name="assume_sorted" value="true" /> <param name="aligned_reads_only" value="false" /> <param name="pf_reads_only" value="false" /> <param name="include_no_calls" value="false" /> <param name="reference_source_selector" value="history" /> <param name="ref_file" value="picard_QualityScoreDistribution_ref.fa" /> <param name="inputFile" value="picard_QualityScoreDistribution.bam" ftype="bam" /> <output name="outFile" file="picard_QualityScoreDistribution_test1.tab" ftype="tabular" lines_diff="4"/> </test> </tests> <help> .. class:: infomark **Purpose** Program to chart quality score distributions in a SAM or BAM dataset. @dataset_collections@ @description@ ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value: false. Possible values: {true, false} PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false. Possible values: {true, false} INCLUDE_NO_CALLS=Boolean If set to true, include quality for no-call bases in the distribution. Default value: false. Possible values: {true, false} ASSUME_SORTED=Boolean AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True @more_info@ </help> </tool>