Mercurial > repos > iuc > varscan_somatic
view macros.xml @ 4:00a6be52a45a draft
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
author | iuc |
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date | Tue, 04 Dec 2018 05:53:45 -0500 |
parents | 2fe9ebb98aad |
children | 4e97191a1ff7 |
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<macros> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">varscan</requirement> <yield/> </requirements> </xml> <token name="@VERSION@">2.4.3</token> <xml name="stdio"> <stdio> <regex match="Exception" source="both" level="fatal" description="Tool exception"/> <regex match=".*" source="both" level="log" description="tool progress"/> </stdio> <version_command><![CDATA[varscan 2>&1 | head -n 1]]></version_command> </xml> <xml name="citations"> <citations> <citation type="doi">10.1101/gr.129684.111</citation> <citation type="doi">10.1002/0471250953.bi1504s44</citation> </citations> </xml> <xml name="input_pileups"> <conditional name="pileup"> <param name="pileup_select" type="select" label="How do you want to provide your pileup files?" help=""> <option value="separated">As separated normal and tumor files</option> <option value="combined">Normal and Tumor combined in one file</option> </param> <when value="separated"> <param name="normal_pileup" format="pileup" type="data" label="Samtools pileup dataset for Normal" help=""/> <param name="tumor_pileup" format="pileup" type="data" label="Samtools pileup dataset for Tumor" help=""/> </when> <when value="combined"> <param name="combined_pileup" format="pileup" type="data" label="Samtools pileup dataset which has combined Normal and Tumor samples" help=""/> </when> </conditional> </xml> <token name="@INPUT_PILEUPS@"> #if $pileup.pileup_select == 'separated' '${pileup.normal_pileup}' '${pileup.tumor_pileup}' galaxy_out #else: '${pileup.combined_pileup}' galaxy_out --mpileup 1 #end if </token> <xml name="min_coverage" token_help="Minimum depth at a position to make a call"> <param argument="--min-coverage" name="min_coverage" type="integer" value="8" min="1" max="200" label="Minimum coverage" help="@HELP@"/> </xml> <xml name="min_reads2"> <param argument="--min-reads2" name="min_reads2" type="integer" value="2" min="1" max="200" label="Minimum supporting reads" help="Minimum number of variant-supporting reads at a position required to make a call"/> </xml> <xml name="min_avg_qual"> <param argument="--min-avg-qual" name="min_avg_qual" type="integer" value="15" min="1" max="50" label="Minimum base quality" help="The minimum base quality at the variant position required to use a read for calling" /> </xml> <xml name="min_var_freq" token_value="0.01"> <param argument="--min-var-freq" name="min_var_freq" type="float" value="@VALUE@" min="0" max="1" label="Minimum variant allele frequency" help="Minimum variant allele frequency required for calling a variant"/> </xml> <xml name="min_freq_for_hom"> <param argument="--min-freq-for-hom" name="min_freq_for_hom" type="float" value="0.75" min="0" max="1" label="Minimum homozygous variant allele frequency" help="Minimum variant allele frequency required for calling a homozygous genotype" /> </xml> <xml name="p_value" token_value="0.01" token_label="p-value threshold for calling variants" token_help=""> <param argument="--p-value" name="p_value" type="float" value="@VALUE@" min="0" max="1" label="@LABEL@" help="@HELP@"/> </xml> <xml name="strand_filter"> <param name="strand_filter" type="select" label="Ignore variants with >90% support on one strand"> <option value="no" selected="True">no</option> <option value="yes">yes</option> </param> </xml> <token name="@HELP_HEADER@"><![CDATA[ **VarScan Overview** VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data. Full documentation of the command line package is available here_. .. _VarScan: http://dkoboldt.github.io/varscan/ .. _here: http://dkoboldt.github.io/varscan/using-varscan.html ]]></token> </macros>