Mercurial > repos > iuc > varscan_somatic

comparison macros.xml @ 7:2ea345eef4e2 draft

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"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156"
author iuc
date Fri, 16 Aug 2019 15:48:18 -0400
parents d0960ef07e55
children
comparison
equal deleted inserted replaced
6:def508f3149e 7:2ea345eef4e2
54 54
55 <xml name="min_coverage" token_help="Minimum depth at a position to make a call"> 55 <xml name="min_coverage" token_help="Minimum depth at a position to make a call">
56 <param argument="--min-coverage" name="min_coverage" type="integer" value="8" min="1" max="200" 56 <param argument="--min-coverage" name="min_coverage" type="integer" value="8" min="1" max="200"
57 label="Minimum coverage" help="@HELP@"/> 57 label="Minimum coverage" help="@HELP@"/>
58 </xml> 58 </xml>
59 <xml name="min_reads2"> 59 <xml name="min_reads2" token_help="Minimum number (default: 2) of variant-supporting reads at a position required to make a call">
60 <param argument="--min-reads2" name="min_reads2" type="integer" value="2" min="1" max="200" 60 <param argument="--min-reads2" name="min_reads2" type="integer" value="2" min="1" max="200"
61 label="Minimum supporting reads" help="Minimum number of variant-supporting reads at a position required to make a call"/> 61 label="Minimum supporting reads" help="@HELP@"/>
62 </xml> 62 </xml>
63 <xml name="min_avg_qual"> 63 <xml name="min_avg_qual">
64 <param argument="--min-avg-qual" name="min_avg_qual" type="integer" value="15" min="1" max="50" 64 <param argument="--min-avg-qual" name="min_avg_qual" type="integer" value="15" min="1" max="50"
65 label="Minimum base quality" 65 label="Minimum base quality"
66 help="The minimum base quality at the variant position required to use a read for calling" /> 66 help="The minimum base quality at the variant position required to use a read for calling" />
67 </xml> 67 </xml>
68 <xml name="min_var_freq" token_value="0.01"> 68 <xml name="min_var_freq" token_value="0.01">
69 <param argument="--min-var-freq" name="min_var_freq" type="float" value="@VALUE@" min="0" max="1" 69 <param argument="--min-var-freq" name="min_var_freq" type="float" value="@VALUE@" min="0" max="1"
70 label="Minimum variant allele frequency" 70 label="Minimum variant allele frequency"
71 help="Minimum variant allele frequency required for calling a variant"/> 71 help="Minimum variant allele frequency (default: @VALUE@) required for calling a variant"/>
72 </xml> 72 </xml>
73 <xml name="min_freq_for_hom"> 73 <xml name="min_freq_for_hom">
74 <param argument="--min-freq-for-hom" name="min_freq_for_hom" type="float" value="0.75" min="0" max="1" 74 <param argument="--min-freq-for-hom" name="min_freq_for_hom" type="float" value="0.75" min="0" max="1"
75 label="Minimum homozygous variant allele frequency" 75 label="Minimum homozygous variant allele frequency"
76 help="Minimum variant allele frequency required for calling a homozygous genotype" /> 76 help="Minimum variant allele frequency (default: 0.75) required for calling a homozygous genotype" />
77 </xml> 77 </xml>
78 <xml name="p_value" token_value="0.01" 78 <xml name="p_value" token_value="0.01"
79 token_label="p-value threshold for calling variants" 79 token_label="p-value threshold for calling variants"
80 token_help=""> 80 token_help="">
81 <param argument="--p-value" name="p_value" type="float" value="@VALUE@" min="0" max="1" 81 <param argument="--p-value" name="p_value" type="float" value="@VALUE@" min="0" max="1"