Mercurial > repos > iuc > varscan_mpileup

comparison macros.xml @ 0:1e667badbe87 draft

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planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
author iuc
date Tue, 10 Jul 2018 13:36:03 -0400
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children 0bc800d67a0e
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-1:000000000000 0:1e667badbe87
1 <macros>
2 <xml name="requirements">
3 <requirements>
4 <requirement type="package" version="@VERSION@">varscan</requirement>
5 <requirement type="package" version="4.2.1">gawk</requirement>
6 <yield/>
7 </requirements>
8 </xml>
9
10 <token name="@VERSION@">2.4.3</token>
11
12 <xml name="stdio">
13 <stdio>
14 <regex match="Exception" source="both" level="fatal" description="Tool exception"/>
15 <regex match=".*" source="both" level="log" description="tool progress"/>
16 </stdio>
17 <version_command><![CDATA[varscan 2>&1 | head -n 1]]></version_command>
18 </xml>
19
20 <xml name="citations">
21 <citations>
22 <citation type="doi">10.1101/gr.129684.111</citation>
23 </citations>
24 </xml>
25
26 <xml name="min_coverage">
27 <param argument="--min-coverage" name="min_coverage" type="integer" value="8" min="1" max="200"
28 label="Minimum read depth" help="Minimum depth at a position to make a call"/>
29 </xml>
30 <xml name="min_reads2">
31 <param argument="--min-reads2" name="min_reads2" type="integer" value="2" min="1" max="200"
32 label="Minimum supporting reads" help="Minimum supporting reads at a position to make a call"/>
33 </xml>
34 <xml name="min_avg_qual">
35 <param argument="--min-avg-qual" name="min_avg_qual" type="integer" value="15" min="1" max="50"
36 label="Minimum base quality at a position to count a read"/>
37 </xml>
38 <xml name="min_var_freq" token_value="0.01">
39 <param argument="--min-var-freq" name="min_var_freq" type="float" value="@VALUE@" min="0" max="1"
40 label="Minimum variant allele frequency threshold"/>
41 </xml>
42 <xml name="min_freq_for_hom">
43 <param argument="--min-freq-for-hom" name="min_freq_for_hom" type="float" value="0.75" min="0" max="1"
44 label="Minimum frequency to call homozygote"/>
45 </xml>
46 <xml name="p_value" token_label="p-value threshold for calling variants" token_value="0.01">
47 <param argument="--p-value" name="p_value" type="float" value="@VALUE@" min="0.0" max="1.0"
48 label="@LABEL@"/>
49 </xml>
50 <xml name="strand_filter">
51 <param name="strand_filter" type="select" label="Ignore variants with >90% support on one strand">
52 <option value="no" selected="True">no</option>
53 <option value="yes">yes</option>
54 </param>
55 </xml>
56
57 </macros>