Mercurial > repos > iuc > lofreq_filter
annotate lofreq_filter.xml @ 4:950d1d49d678 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 841c48994eb214a2f8718b1d1aca22bc38598528"
author | iuc |
---|---|
date | Mon, 15 Jun 2020 13:12:17 -0400 |
parents | fdba1586551d |
children | 7dfca164d2e3 |
rev | line source |
---|---|
4
950d1d49d678
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 841c48994eb214a2f8718b1d1aca22bc38598528"
iuc
parents:
1
diff
changeset
|
1 <tool id="lofreq_filter" name="Lofreq filter" version="@TOOL_VERSION@+galaxy0"> |
0
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
2 <description>called variants posteriorly</description> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
3 <macros> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
4 <import>macros.xml</import> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
5 <xml name="snvqual_filter_config"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
6 <conditional name="snvqual_filter"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
7 <param name="snvqual" type="select" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
8 label="Filter SNVs based on call quality?"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
9 <option value="no">No, don't apply call quality filter</option> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
10 <option value="min-phred">Yes, filter on explicit QUAL threshold</option> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
11 <option value="mtc">Yes, filter on multiple testing corrected p-value</option> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
12 </param> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
13 <when value="no"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
14 </when> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
15 <when value="min-phred"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
16 <param argument="-Q" name="snvqual_thresh" type="integer" min="0" value="0" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
17 label="Minimum QUAL value" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
18 help="Specify the minimum value of the QUAL field required to retain a variant" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
19 </when> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
20 <when value="mtc"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
21 <param argument="-r" name="snvqual_alpha" type="float" min="0" max="1" value="1" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
22 label="Multiple-testing corrected p-value threshold" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
23 <param argument="-q" name="snvqual_mtc" type="select" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
24 label="Multiple testing correction method"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
25 <option value="bonf">Bonferroni</option> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
26 <option value="holm">Holm-Sidak</option> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
27 <option value="fdr">False-discovery rate</option> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
28 </param> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
29 <param argument="-s" name="snvqual_ntests" type="integer" min="1" value="1" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
30 label="Estimate of number of tests performed" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
31 help="Ideally, this would be the number of SNVs considered during variant calling. The lofreq variant caller emits this number as part of its output. For other variant callers, all you will typically have is a lower bound estimate given by the number of SNV records in your VCF input." /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
32 </when> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
33 </conditional> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
34 </xml> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
35 <xml name="indelqual_filter_config"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
36 <conditional name="indelqual_filter"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
37 <param name="indelqual" type="select" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
38 label="Filter indels based on call quality?"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
39 <option value="no">No, don't apply call quality filter</option> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
40 <option value="min-phred">Yes, filter on explicit QUAL threshold</option> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
41 <option value="mtc">Yes, filter on multiple testing corrected p-value</option> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
42 </param> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
43 <when value="no"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
44 </when> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
45 <when value="min-phred"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
46 <param argument="-K" name="indelqual_thresh" type="integer" min="0" value="0" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
47 label="Minimum QUAL value" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
48 help="Specify the minimum value of the QUAL field required to retain a variant" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
49 </when> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
50 <when value="mtc"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
51 <param argument="-l" name="indelqual_alpha" type="float" min="0" max="1" value="1" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
52 label="Multiple-testing corrected p-value threshold" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
53 <param argument="-k" name="indelqual_mtc" type="select" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
54 label="Multiple testing correction method"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
55 <option value="bonf">Bonferroni</option> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
56 <option value="holm">Holm-Sidak</option> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
57 <option value="fdr">False-discovery rate</option> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
58 </param> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
59 <param argument="-m" name="indelqual_ntests" type="integer" min="1" value="1" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
60 label="Estimate of number of tests performed" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
61 help="Ideally, this would be the number of indels considered during variant calling. The lofreq variant caller emits this number as part of its output. For other variant callers, all you will typically have is a lower bound estimate given by the number of indel records in your VCF input." /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
62 </when> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
63 </conditional> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
64 </xml> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
65 </macros> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
66 <expand macro="requirements" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
67 <command detect_errors="exit_code"><![CDATA[ |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
68 ## filter variants with lofreq |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
69 lofreq filter -i $invcf --no-defaults --verbose |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
70 $flag_or_drop |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
71 ${filter_by_type.keep_only} |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
72 #if str($filter_by_type.keep_only) in ['', '--only-snvs']: |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
73 #if str($filter_by_type.qual.snvqual_filter.snvqual) == 'min-phred': |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
74 -Q ${filter_by_type.qual.snvqual_filter.snvqual_thresh} |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
75 #elif str($filter_by_type.qual.snvqual_filter.snvqual) == 'mtc': |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
76 -q ${filter_by_type.qual.snvqual_filter.snvqual_mtc} |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
77 -r ${filter_by_type.qual.snvqual_filter.snvqual_alpha} |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
78 -s ${filter_by_type.qual.snvqual_filter.snvqual_ntests} |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
79 #end if |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
80 #end if |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
81 #if str($filter_by_type.keep_only) in ['', '--only-indels']: |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
82 #if str($filter_by_type.qual.indelqual_filter.indelqual) == 'min-phred': |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
83 -K ${filter_by_type.qual.indelqual_filter.indelqual_thresh} |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
84 #elif str($filter_by_type.qual.indelqual_filter.indelqual) == 'mtc': |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
85 -k ${filter_by_type.qual.indelqual_filter.indelqual_mtc} |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
86 -l ${filter_by_type.qual.indelqual_filter.indelqual_alpha} |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
87 -m ${filter_by_type.qual.indelqual_filter.indelqual_ntests} |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
88 #end if |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
89 #end if |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
90 -v ${coverage.cov_min} |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
91 -V ${coverage.cov_max} |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
92 -a ${af.af_min} |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
93 -A ${af.af_max} |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
94 #if str($sb.sb_filter.strand_bias) == 'max-phred': |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
95 -B ${sb.sb_filter.sb_thresh} |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
96 #elif str($sb.sb_filter.strand_bias) == 'mtc': |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
97 -b ${sb.sb_filter.sb_mtc} |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
98 -c ${sb.sb_filter.sb_alpha} |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
99 #end if |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
100 #if str($sb.sb_filter.strand_bias) != 'no': |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
101 ${sb.sb_filter.sb_compound} |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
102 ${sb.sb_filter.sb_indels} |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
103 #end if |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
104 -o filtered.vcf |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
105 ]]></command> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
106 <inputs> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
107 <param argument="-i" name="invcf" type="data" format="vcf,vcf_bgzip" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
108 label="List of variants to filter" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
109 <conditional name="filter_by_type"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
110 <param name="keep_only" type="select" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
111 label="Types of variants to keep"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
112 <option value="">SNVs and Indels</option> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
113 <option value="--only-snvs">SNVs only</option> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
114 <option value="--only-indels">Indels only</option> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
115 </param> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
116 <when value=""> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
117 <section name="qual" title="Quality-based filter options" expanded="True"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
118 <expand macro="snvqual_filter_config" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
119 <expand macro="indelqual_filter_config" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
120 </section> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
121 </when> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
122 <when value="--only-snvs"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
123 <section name="qual" title="Quality-based filter options" expanded="True"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
124 <expand macro="snvqual_filter_config" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
125 </section> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
126 </when> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
127 <when value="--only-indels"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
128 <section name="qual" title="Quality-based filter options" expanded="True"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
129 <expand macro="indelqual_filter_config" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
130 </section> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
131 </when> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
132 </conditional> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
133 <section name="coverage" title="Coverage-based filter options" expanded="True" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
134 help="You can specify a range of acceptable coverage values at variant sites by setting minimum and maximum coverage. Set either value to zero to make the range unbounded on the corresponding side, or disable filtering based on coverage by setting both values to zero."> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
135 <param argument="-v" name="cov_min" type="integer" min="0" value="10" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
136 label="Minimum coverage" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
137 help="The minimum coverage at a site required to keep variants" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
138 <param argument="-V" name="cov_max" type="integer" min="0" value="0" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
139 label="Maximum coverage" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
140 help="The maximum coverage at a site allowed to keep variants" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
141 </section> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
142 <section name="af" title="Allele frequency filter options" expanded="True" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
143 help="You can specify a range of acceptable allele frequencies at variant sites by setting minimum and maximum AF values. Set either value to zero to make the range unbounded on the corresponding side, or disable filtering based on allele frequency by setting both values to zero."> |
1
fdba1586551d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
iuc
parents:
0
diff
changeset
|
144 <param argument="-a" name="af_min" type="float" min="0" max="1" value="0" |
0
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
145 label="Minimum allele frequency" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
146 help="To keep a variant its allele needs to be observed at this frequency at least." /> |
1
fdba1586551d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9e41ac63171c3e3a6fd2b4d018d0c60c9f1fbae1"
iuc
parents:
0
diff
changeset
|
147 <param argument="-A" name="af_max" type="float" min="0" max="1" value="0" |
0
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
148 label="Maximum allele frequency" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
149 help="To keep a variant its allele is allowed to be observed at this frequency at most." /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
150 </section> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
151 <section name="sb" title="Strand bias filter options" expanded="True"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
152 <conditional name="sb_filter"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
153 <param name="strand_bias" type="select" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
154 label="Filter variants based on supporting strand bias?"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
155 <option value="no">No, don't apply strand-bias filter</option> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
156 <option value="max-phred">Yes, filter on explicit SB threshold</option> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
157 <option value="mtc" selected="True">Yes, filter on multiple testing corrected strand-bias p-value (lofreq default)</option> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
158 </param> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
159 <when value="no"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
160 </when> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
161 <when value="max-phred"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
162 <param argument="-B" name="sb_thresh" type="integer" min="0" value="0" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
163 label="" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
164 </when> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
165 <when value="mtc"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
166 <param argument="-c" name="sb_alpha" type="float" min="0" max="1" value="0.001" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
167 label="Multiple-testing corrected p-value threshold" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
168 <param argument="-b" name="sb_mtc" type="select" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
169 label="Multiple testing correction method"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
170 <option value="bonf">Bonferroni</option> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
171 <option value="holm">Holm-Sidak</option> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
172 <option value="fdr" selected="True">False-discovery rate</option> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
173 </param> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
174 <param name="sb_compound" type="boolean" checked="True" truevalue="" falsevalue="--sb-no-compound" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
175 label="Use compound strand-bias filter?" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
176 help="With compound filtering a variant is filtered only if it fails the strand-bias filter configured above AND has 85% of its supporting reads mapped to one reference genome strand. This guards against filtering based on statistically significant, but minor strand bias effects at high-coverage sites." /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
177 <param argument="--sb-incl-indels" name="sb_indels" type="boolean" checked="False" truevalue="--sb-incl-indels" falsevalue="" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
178 label="Apply to indels?" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
179 help="By default, indels are not filtered based on strand bias." /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
180 </when> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
181 </conditional> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
182 </section> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
183 <param argument="--print-all" name="flag_or_drop" type="select" display="radio" |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
184 label="Action to be taken for variants that do not pass the filters defined above"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
185 <option value="">Drop variants not passing one or more filters</option> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
186 <option value="--print-all">Keep variants, but indicate failed filters in output FILTER column</option> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
187 </param> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
188 </inputs> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
189 <outputs> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
190 <data name="outvcf" format="vcf" from_work_dir="filtered.vcf"/> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
191 </outputs> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
192 <tests> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
193 <test> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
194 <!-- Mimick lofreq call default filtering --> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
195 <param name="invcf" ftype="vcf" value="call-out2.vcf" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
196 <conditional name="filter_by_type"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
197 <section name="qual"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
198 <conditional name="snvqual_filter"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
199 <param name="snvqual" value="min-phred" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
200 <param name="snvqual_thresh" value="38" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
201 </conditional> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
202 <conditional name="indelqual_filter"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
203 <param name="indelqual" value="min-phred" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
204 <param name="indelqual_thresh" value="20" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
205 </conditional> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
206 </section> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
207 </conditional> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
208 <!-- lofreq call writes duplicate ##FILTER declarations, while |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
209 lofreq filter behaves correctly. => two additional diff lines --> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
210 <output name="outvcf" file="call-out1.vcf" lines_diff="6" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
211 </test> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
212 <test> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
213 <!-- Express lofreq call default filtering as a |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
214 multiple testing correction filter --> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
215 <param name="invcf" ftype="vcf" value="call-out2.vcf" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
216 <conditional name="filter_by_type"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
217 <param name="keep_only" value="--only-snvs" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
218 <section name="qual"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
219 <conditional name="snvqual_filter"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
220 <param name="snvqual" value="mtc" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
221 <param name="snvqual_alpha" value="0.01" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
222 <param name="snvqual_mtc" value="bonf" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
223 <param name="snvqual_ntests" value="66" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
224 </conditional> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
225 </section> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
226 </conditional> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
227 <!-- expect additional diff lines because of different |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
228 ##FILTER declarations --> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
229 <output name="outvcf" file="call-out1.vcf" lines_diff="9" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
230 </test> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
231 <test> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
232 <!-- Test print-all option --> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
233 <param name="invcf" ftype="vcf" value="call-out2.vcf" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
234 <conditional name="filter_by_type"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
235 <section name="qual"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
236 <conditional name="snvqual_filter"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
237 <param name="snvqual" value="min-phred" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
238 <param name="snvqual_thresh" value="38" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
239 </conditional> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
240 <conditional name="indelqual_filter"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
241 <param name="indelqual" value="min-phred" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
242 <param name="indelqual_thresh" value="20" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
243 </conditional> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
244 </section> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
245 </conditional> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
246 <param name="flag_or_drop" value="--print-all" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
247 <!-- All variants should be retained with print-all, |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
248 but variants failing filters should be flagged with the names |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
249 of those filters --> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
250 <output name="outvcf"> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
251 <assert_contents> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
252 <has_line_matching expression="pBR322	1134	.	C	T	49314	PASS	.+" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
253 <has_line_matching expression="pBR322	1193	.	G	A	0	min_snvqual_38	.+" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
254 </assert_contents> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
255 </output> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
256 </test> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
257 </tests> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
258 <help><![CDATA[ |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
259 **What it does** |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
260 |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
261 **Lofreq filter** tries to eliminate false-positive calls from a list of |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
262 variants in VCF format. |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
263 |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
264 To this end, it applies a variety of user-configurable filters to the input |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
265 variants, which all operate on variant attributes expected to be embedded in |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
266 the VCF input. |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
267 |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
268 Specifically, certain filters expect: |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
269 |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
270 - the `QUAL` field of the variant records to be set |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
271 - any of the following subfields of a variant's `INFO` field: |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
272 |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
273 * `DP` (required for coverage-based filtering) |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
274 * `AF` (required for filtering based on variant allele frequency) |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
275 * `SB` (required for filtering on strand bias) |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
276 * `DP4` (required for the compound strand bias filter) |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
277 |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
278 ------ |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
279 |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
280 **Note**: |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
281 |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
282 .. class:: Warning mark |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
283 |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
284 This tool is optimized for posterior filtering of variants called with |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
285 `Lofreq call`, which outputs all variant attributes required by the various |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
286 configurable filters. |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
287 |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
288 If you are using `Lofreq filter` to filter VCF variant lists produced with |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
289 other tools, be prepared for surprises. |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
290 |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
291 In general, if any piece of variant information required for applying a |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
292 given filter is missing from the input data, the tool will try to disable |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
293 that filter. Watch out for corresponding warnings in the tool's standard |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
294 output. |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
295 |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
296 In addition, any p-value based filtering on variant qualities may behave |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
297 incorrectly since different variant callers might use different QUAL scales. |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
298 ]]></help> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
299 <expand macro="citations" /> |
6f9ffff040ce
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff
changeset
|
300 </tool> |