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comparison macros.xml @ 2:d0960ef07e55 draft

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planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
author iuc
date Tue, 04 Dec 2018 06:10:19 -0500
parents fd901d18b081
children 2ea345eef4e2
comparison
equal deleted inserted replaced
1:fd901d18b081 2:d0960ef07e55
1 <macros> 1 <macros>
2 <xml name="requirements"> 2 <xml name="requirements">
3 <requirements> 3 <requirements>
4 <requirement type="package" version="@VERSION@">varscan</requirement> 4 <requirement type="package" version="@VERSION@">varscan</requirement>
5 <requirement type="package" version="4.2.1">gawk</requirement>
6 <yield/> 5 <yield/>
7 </requirements> 6 </requirements>
8 </xml> 7 </xml>
9 8
10 <token name="@VERSION@">2.4.3</token> 9 <token name="@VERSION@">2.4.3</token>
18 </xml> 17 </xml>
19 18
20 <xml name="citations"> 19 <xml name="citations">
21 <citations> 20 <citations>
22 <citation type="doi">10.1101/gr.129684.111</citation> 21 <citation type="doi">10.1101/gr.129684.111</citation>
22 <citation type="doi">10.1002/0471250953.bi1504s44</citation>
23 </citations> 23 </citations>
24 </xml> 24 </xml>
25 25
26 <xml name="input_pileups"> 26 <xml name="input_pileups">
27 <conditional name="pileup"> 27 <conditional name="pileup">
50 --mpileup 1 50 --mpileup 1
51 #end if 51 #end if
52 52
53 </token> 53 </token>
54 54
55 <xml name="min_coverage"> 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 read depth" help="Minimum depth at a position to make a call"/> 57 label="Minimum coverage" help="@HELP@"/>
58 </xml> 58 </xml>
59 <xml name="min_reads2"> 59 <xml name="min_reads2">
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 supporting reads at a position to make a call"/> 61 label="Minimum supporting reads" help="Minimum number of variant-supporting reads at a position required to make a call"/>
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 at a position to count a read"/> 65 label="Minimum base quality"
66 help="The minimum base quality at the variant position required to use a read for calling" />
66 </xml> 67 </xml>
67 <xml name="min_var_freq" token_value="0.01"> 68 <xml name="min_var_freq" token_value="0.01">
68 <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"
69 label="Minimum variant allele frequency threshold"/> 70 label="Minimum variant allele frequency"
71 help="Minimum variant allele frequency required for calling a variant"/>
70 </xml> 72 </xml>
71 <xml name="min_freq_for_hom"> 73 <xml name="min_freq_for_hom">
72 <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"
73 label="Minimum frequency to call homozygote"/> 75 label="Minimum homozygous variant allele frequency"
76 help="Minimum variant allele frequency required for calling a homozygous genotype" />
74 </xml> 77 </xml>
75 <xml name="p_value" token_label="p-value threshold for calling variants" token_value="0.01"> 78 <xml name="p_value" token_value="0.01"
76 <param argument="--p-value" name="p_value" type="float" value="@VALUE@" min="0.0" max="1.0" 79 token_label="p-value threshold for calling variants"
77 label="@LABEL@"/> 80 token_help="">
81 <param argument="--p-value" name="p_value" type="float" value="@VALUE@" min="0" max="1"
82 label="@LABEL@" help="@HELP@"/>
78 </xml> 83 </xml>
79 <xml name="strand_filter"> 84 <xml name="strand_filter">
80 <param name="strand_filter" type="select" label="Ignore variants with >90% support on one strand"> 85 <param name="strand_filter" type="select" label="Ignore variants with >90% support on one strand">
81 <option value="no" selected="True">no</option> 86 <option value="no" selected="True">no</option>
82 <option value="yes">yes</option> 87 <option value="yes">yes</option>
83 </param> 88 </param>
84 </xml> 89 </xml>
85 90
91 <token name="@HELP_HEADER@"><![CDATA[
92 **VarScan Overview**
93
94 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_.
95
96 .. _VarScan: http://dkoboldt.github.io/varscan/
97 .. _here: http://dkoboldt.github.io/varscan/using-varscan.html
98 ]]></token>
86 </macros> 99 </macros>