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comparison filter_vcf.xml @ 0:834a312c0114 draft

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author ulfschaefer
date Thu, 10 Dec 2015 09:22:39 -0500
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-1:000000000000 0:834a312c0114
1 <tool id="filter_vcf" name="Filter VCF" version="1.0">
2 <description>filters a VCF file</description>
3 <requirements>
4 <requirement type="package" version="2.7.10">python</requirement>
5 <requirement type="package" version="0.6.7">pyvcf</requirement>
6 <requirement type="package" version="3.11">pyyaml</requirement>
7 </requirements>
8 <stdio>
9 <!-- Assume anything other than zero is an error -->
10 <exit_code range="1:" />
11 <exit_code range=":-1" />
12 </stdio>
13 <command interpreter="bash">
14 filter_vcf.sh
15 $output
16 $input
17 #for $sf in $snp_filter:
18 #for $name, $param in $sf.snp_filter_type.iteritems():
19 #if $name not in [ "__current_case__", "snp_filter_type_selector" ]:
20 ${name}:"${param}"
21 #end if
22 #end for
23 #end for
24 </command>
25
26 <inputs>
27 <param name="input" type="data" format="vcf" label="VCF File to filter" />
28
29 <repeat name="snp_filter" title="SNP Filter" help="">
30 <conditional name="snp_filter_type">
31 <param name="snp_filter_type_selector" type="select" label="SNP Filter Type">
32 <option value="gq_score_option">GQ score</option>
33 <option value="dp4_ratio_option">DP4 ratio</option>
34 <option value="ad_ratio_option">AD ratio</option>
35 <option value="mq_score_option">MQ score</option>
36 <option value="min_depth_option">Minimum depth</option>
37 <option value="uncall_gt_option">Uncall GT</option>
38 <option value="mq0_ratio_option">MQ0 ratio</option>
39 <option value="qual_score_option">Quality score</option>
40 <option value="mq0f_ratio_option">MQ0F ratio</option>
41 </param>
42 <when value="gq_score_option">
43 <param name="gq_score" type="integer" value="0" label="Minimum GC score" help="Type integer"/>
44 </when>
45 <when value="dp4_ratio_option">
46 <param name="dp4_ratio" type="float" value="0.9" label="Minimum DP4 ratio" help="Type float"/>
47 </when>
48 <when value="ad_ratio_option">
49 <param name="ad_ratio" type="float" value="0.9" label="Minimum AD ratio" help="Type float"/>
50 </when>
51 <when value="mq_score_option">
52 <param name="mq_score" type="integer" value="30" label="Minimum MQ score" help="Type integer"/>
53 </when>
54 <when value="min_depth_option">
55 <param name="min_depth" type="integer" value="5" label="Minimum depth" help="Type integer"/>
56 </when>
57 <when value="uncall_gt_option">
58 <param name="uncall_gt" type="text" value="" hidden="True"/>
59 </when>
60 <when value="mq0_ratio_option">
61 <param name="mq0_ratio" type="float" value="0.05" label="Minimim MQ0 ratio" help="Type float"/>
62 </when>
63 <when value="qual_score_option">
64 <param name="qual_score" type="integer" value="30" label="Minimim quality score" help="Type integer"/>
65 </when>
66 <when value="mq0f_ratio_option">
67 <param name="mq0f_ratio" type="float" value="0.05" label="Minimum MQ0F ratio" help="Type float"/>
68 </when>
69 </conditional>
70 </repeat>
71
72 </inputs>
73
74 <outputs>
75 <data format="vcf" name="output" label="${tool.name} on ${on_string}: filtered VCF" />
76 </outputs>
77 <tests>
78 <test>
79 <param name="input" value="test_input.vcf" ftype="vcf" />
80 <param name="min_depth" value="100" />
81 <output name="output" file="test_output.vcf" ftype="vcf" />
82 </test>
83 </tests>
84 <help>
85
86 usage: filter_vcf.py [-h] \-\-vcf VCF \-\-filters FILTERS \-\-output OUTPUT
87
88 optional arguments:
89
90 -h, \-\-help show this help message and exit
91
92 \-\-vcf VCF, -v VCF VCF file to (re)filter.
93
94 \-\-filters FILTERS, -f FILTERS Filter(s) to apply as key:threshold pairs, separated by comma.
95
96 \-\-output OUTPUT, -o OUTPUT Location for filtered VCF to be written.
97
98 </help>
99 </tool>