Mercurial > repos > devteam > picard
view picard_MeanQualityByCycle.xml @ 17:2474cd44d10a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
author | iuc |
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date | Fri, 29 Mar 2019 08:31:40 -0400 |
parents | a5a13ea16d17 |
children | c943f4a04af0 |
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<tool name="MeanQualityByCycle" id="picard_MeanQualityByCycle" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>chart distribution of base qualities</description> <macros> <import>picard_macros.xml</import> <token name="@WRAPPER_VERSION@">1</token> </macros> <expand macro="requirements"> <requirement type="package" version="3.4.1">r-base</requirement> </expand> <command detect_errors="exit_code"><![CDATA[ @java_options@ ##set up input files @symlink_element_identifier@ #set $reference_fasta_filename = "localref.fa" @handle_reference_source@ picard MeanQualityByCycle INPUT='$escaped_element_identifier' OUTPUT="${outFile}" CHART_OUTPUT="${pdfFile}" REFERENCE_SEQUENCE="${reference_fasta_filename}" ALIGNED_READS_ONLY="${aligned_reads_only}" PF_READS_ONLY="${pf_reads_only}" ASSUME_SORTED="${assume_sorted}" VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR @TMPDIR_OPTION@ ]]></command> <inputs> <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/> <conditional name="reference_source"> <param name="reference_source_selector" type="select" label="Load reference genome from"> <option value="cached">Local cache</option> <option value="history">History</option> </param> <when value="cached"> <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> <options from_data_table="all_fasta"> </options> <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> </param> </when> <when value="history"> <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> </when> </conditional> <param name="aligned_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true, calculate mean quality over aligned reads only" help="ALIGNED_READS_ONLY; default=False"/> <param name="pf_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true calculate mean quality over reads passing quality filter" help="PF_READS_ONLY; default=False"/> <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> <expand macro="VS" /> </inputs> <outputs> <data format="tabular" name="outFile" label="${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="reference_source_selector" value="history" /> <param name="ref_file" value="picard_MeanQualityByCycle_ref.fa" /> <param name="inputFile" value="picard_MeanQualityByCycle.bam" ftype="bam" /> <output name="outFile" file="picard_MeanQualityByCycle_test1.tab" ftype="tabular" lines_diff="4"/> </test> </tests> <help> .. class:: infomark **Purpose** Program to chart the distribution of base qualities by cycle within reads supplied 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. This option can be set to 'null' to clear the default value. 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> <expand macro="citations" /> </tool>