Mercurial > repos > iuc > varscan_mpileup
view varscan_mpileup.xml @ 5:d7e6c347538d draft
planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934
author | iuc |
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date | Wed, 05 Dec 2018 11:17:06 -0500 |
parents | d062703d6f13 |
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<tool id="varscan_mpileup" name="VarScan mpileup" version="@VERSION@.1"> <description>for variant detection</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> <requirement type="package" version="4.2.1">gawk</requirement> </expand> <expand macro="stdio" /> <command><![CDATA[ ## Set up samples list file. #if $sample_names.strip() != '': echo $sample_names | awk -F ',' '{ for (i = 1; i <= NF; i++) { print \$i; } }' > samples_list.txt && #end if ## Set up command + input. varscan ${cmd} '${input}' --min-coverage ${min_coverage} --min-reads2 ${min_reads2} --min-avg-qual ${min_avg_qual} --min-var-freq ${min_var_freq} --min-freq-for-hom ${min_freq_for_hom} --p-value ${p_value} #if str($strand_filter) == 'yes': --strand-filter 1 #end if ## Report only variants in consensus. #if str($cmd) == 'mpileup2cns': --variants #end if ## Set up outputs. --output-vcf 1 > '$output' #if $sample_names.strip() != '': --vcf-sample-list samples_list.txt #end if ]]></command> <inputs> <param name="input" format="pileup" type="data" label="Samtools pileup dataset" help=""/> <param name="cmd" type="select" label="Analysis type"> <option value="mpileup2snp" selected="True">single nucleotide variation</option> <option value="mpileup2indel">insertions and deletions</option> <option value="mpileup2cns">consensus genotype</option> </param> <expand macro="min_coverage" /> <expand macro="min_reads2" /> <expand macro="min_avg_qual" /> <expand macro="min_var_freq" value="0.01" /> <expand macro="min_freq_for_hom" /> <expand macro="p_value" value="0.99" label="Default p-value threshold for calling variants"/> <expand macro="strand_filter" /> <param name="sample_names" type="text" value="" help="Separate sample names by comma; leave blank to use default sample names."/> </inputs> <outputs> <data name="output" format="vcf"/> </outputs> <tests> <test> <param name="input" value="test_in1.pileup" /> <param name="cmd" value="mpileup2cns" /> <param name="min_coverage" value="8" /> <param name="min_reads2" value="2" /> <param name="min_avg_qual" value="15" /> <param name="min_var_freq" value="0.01" /> <param name="min_freq_for_hom" value="0.75" /> <param name="p_value" value="0.99" /> <param name="strand_filter" value="no" /> <param name="sample_names" value="" /> <output name="output" file="varscan_mpileup_result1.vcf" lines_diff="0" /> </test> </tests> <help><![CDATA[ @HELP_HEADER@ **Input** :: mpileup file - The SAMtools mpileup file **Output** VarScan produces a VCF 4.1 dataset as output. ]]></help> <expand macro="citations" /> </tool>