Mercurial > repos > artbio > artbio_mutect2

annotate macros.xml @ 0:504de035ac0f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
author artbio
date Thu, 07 May 2020 12:29:36 -0400
parents
children 2b6ee93fd144
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
1 <?xml version="1.0"?>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
2 <macros>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
3 <token name="@VERSION@">4.1.4.0</token>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
4 <token name="@WRAPPER_VERSION@">@VERSION@+galaxy1</token>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
5
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
6 <xml name="requirements">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
7 <requirements>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
8 <requirement type="package" version="@VERSION@">gatk4</requirement>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
9 <requirement type="package" version="0.2.5">tabix</requirement>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
10 <requirement type="package" version="1.9">samtools</requirement>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
11 <yield />
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
12 </requirements>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
13 </xml>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
14
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
15 <!--Hacky way to determine GATK version, for display in tool info-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
16 <xml name="version_cmd">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
17 <version_command>gatk SortSam --version 2>&amp;1 | grep Version | cut -d ':' -f 2</version_command>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
18 </xml>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
19
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
20 <!--Define sections that parameters could exist within.-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
21 <template name="set_sections">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
22 #set global $sections = ['', 'optional.', 'advanced.', 'deprecated.']
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
23 </template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
24
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
25 <!--Reference genome handling-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
26 <!--One template each for the different reference genome parameter names.-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
27 <!--TODO: Can the reference parameters all be the same?-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
28 <xml name="ref_sel">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
29 <conditional name="reference_source">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
30 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
31 <option value="cached">Locally cached</option>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
32 <option value="history">History</option>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
33 <option value="no_ref" selected="true">Do not pass</option>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
34 </param>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
35 <when value="cached">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
36 <param name="reference_sequence" type="select" label="Reference" help="Reference sequence file." >
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
37 <options from_data_table="all_fasta" >
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
38 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
39 </options>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
40 </param>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
41 </when>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
42 <when value="history">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
43 <param name="reference_sequence" type="data" format="fasta" label="Reference" help="Reference sequence file." />
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
44 </when>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
45 <when value="no_ref" />
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
46 </conditional>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
47 </xml>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
48
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
49 <template name="ref_opts">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
50 #for $sect in $sections
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
51 #if $varExists($sect + "reference_source.reference_source_selector")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
52 #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
53 #if $getVar($sect + "reference_source.reference_source_selector") != "history"
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
54 --reference $getVar($sect + "reference_source.reference_sequence.fields.path")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
55 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
56 --reference reference.fa
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
57 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
58 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
59 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
60 #end for
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
61 </template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
62
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
63 <template name="picard_ref_opts">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
64 #for $sect in $sections
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
65 #if $varExists($sect + "reference_source.reference_source_selector")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
66 #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
67 #if $getVar($sect + "reference_source.reference_source_selector") != "history"
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
68 --REFERENCE_SEQUENCE $getVar($sect + "reference_source.reference_sequence.fields.path")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
69 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
70 --REFERENCE_SEQUENCE $getVar($sect + "reference_source.reference_sequence")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
71 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
72 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
73 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
74 #end for
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
75 </template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
76
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
77 <template name="picard_ref_opts_plain">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
78 #for $sect in $sections
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
79 #if $varExists($sect + "reference_source.reference_source_selector")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
80 #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
81 #if $getVar($sect + "reference_source.reference_source_selector") != "history"
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
82 --REFERENCE $getVar($sect + "reference_source.reference_sequence.fields.path")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
83 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
84 --REFERENCE $getVar($sect + "reference_source.reference_sequence")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
85 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
86 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
87 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
88 #end for
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
89 </template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
90
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
91 <template name="ref_opts_input">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
92 #for $sect in $sections
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
93 #if $varExists($sect + "reference_source.reference_source_selector")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
94 #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
95 #if $getVar($sect + "reference_source.reference_source_selector") != "history"
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
96 --input $getVar($sect + "reference_source.reference_sequence.fields.path")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
97 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
98 --input $getVar($sect + "reference_source.reference_sequence")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
99 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
100 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
101 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
102 #end for
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
103 </template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
104
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
105
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
106 <!--Interval Macros-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
107 <template name="gatk_ints_chth">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
108 #for $sect in $sections
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
109 #if $varExists($sect + "ival_type.ival_type_sel")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
110 #if $getVar($sect + "ival_type.ival_type_sel") == "ival_file"
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
111 #if $varExists($sect + "ival_type.intervals")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
112 #if $getVar($sect + "ival_type.intervals").is_of_type("gatk_interval")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
113 --intervals intervals.interval_list
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
114 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
115 #if $getVar($sect + "ival_type.intervals").is_of_type("bed")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
116 --intervals intervals.bed
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
117 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
118 #if $getVar($sect + "ival_type.intervals").is_of_type("vcf")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
119 --intervals intervals.vcf
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
120 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
121 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
122 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
123 #if $varExists($sect + "ival_type.intervals")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
124 --intervals $getVar($sect + "ival_type.intervals")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
125 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
126 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
127 #if $varExists($sect + "ival_type.interval_padding")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
128 --interval-padding $getVar($sect + "ival_type.interval_padding")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
129 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
130 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
131 #end for
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
132 </template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
133
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
134
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
135 <template name="pre_gatk_ints_chth"><![CDATA[
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
136 #for $sect in $sections
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
137 #if $varExists($sect + "ival_type.ival_type_sel")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
138 #if $getVar($sect + "ival_type.ival_type_sel") == "ival_file"
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
139 #if $varExists($sect + "ival_type.intervals")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
140 #if $getVar($sect + "ival_type.intervals").is_of_type("gatk_interval")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
141 ln -s $getVar($sect + "ival_type.intervals") intervals.interval_list &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
142 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
143 #if $getVar($sect + "ival_type.intervals").is_of_type("bed")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
144 ln -s $getVar($sect + "ival_type.intervals") intervals.bed &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
145 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
146 #if $getVar($sect + "ival_type.intervals").is_of_type("vcf")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
147 ln -s $getVar($sect + "ival_type.intervals") intervals.vcf &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
148 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
149 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
150 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
151 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
152 #end for
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
153 ]]></template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
154
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
155 <xml name="gatk_ints">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
156 <conditional name="ival_type">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
157 <param name="ival_type_sel" type="select" label="Choose Genomic Interval Source">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
158 <option value="ival_file" selected="true">Interval File</option>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
159 <option value="ival_text" selected="false">Interval Text Input</option>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
160 </param>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
161 <when value="ival_file">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
162 <param name="intervals" argument="--intervals" type="data" optional="true" format="bed,vcf,gatk_interval" label="Intervals File" help="One or more genomic intervals over which to operate"/>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
163 <param name="interval_padding" argument="--interval-padding" type="integer" optional="true" value="0" label="Interval Padding" help="Amount of padding (in bp) to add to each interval you are including."/>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
164 </when>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
165 <when value="ival_text">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
166 <param name="intervals" argument="--intervals" type="text" optional="true" label="Intervals Text Input" help="One or more genomic intervals over which to operate. Enter in chrom:start-stop format."/>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
167 <param name="interval_padding" argument="--interval-padding" type="integer" optional="true" value="0" label="Interval Padding" help="Amount of padding (in bp) to add to each interval you are including."/>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
168 </when>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
169 </conditional>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
170 </xml>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
171
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
172
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
173 <!--Exclude Intervals-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
174 <xml name="gatk_excl_ints">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
175 <conditional name="excl_ival_type">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
176 <param name="excl_ival_type_sel" type="select" label="Choose Genomic Interval Exclusion Source">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
177 <option value="excl_ival_file" selected="true">Exclude Interval File</option>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
178 <option value="excl_ival_text" selected="false">Exclude Interval Text Input</option>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
179 </param>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
180 <when value="excl_ival_file">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
181 <param name="exclude_intervals" argument="--exclude-intervals" type="data" optional="true" format="bed,vcf,gatk_interval" label="Exclude Intervals File" help="One or more genomic intervals to exclude from processing"/>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
182 <param name="interval_exclusion_padding" argument="--interval-exclusion-padding" type="integer" optional="true" value="0" label="Interval Exclusion Padding" help="Amount of padding (in bp) to add to each interval you are excluding."/>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
183 </when>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
184 <when value="excl_ival_text">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
185 <param name="exclude_intervals" argument="--exclude-intervals" type="text" optional="true" label="Exclude Intervals Text Input" help="One or more genomic intervals to exclude from processing. Enter in chrom:start-stop format."/>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
186 <param name="interval_exclusion_padding" argument="--interval-exclusion-padding" type="integer" optional="true" value="0" label="Interval Exclusion Padding" help="Amount of padding (in bp) to add to each interval you are excluding."/>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
187 </when>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
188 </conditional>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
189 </xml>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
190
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
191 <template name="gatk_excl_ints_chth">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
192 #for $sect in $sections
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
193 #if $varExists($sect + "excl_ival_type.excl_ival_type_sel")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
194 #if $getVar($sect + "excl_ival_type.excl_ival_type_sel") == "ival_file"
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
195 #if $varExists($sect + "excl_ival_type.exclude_intervals")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
196 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("gatk_interval")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
197 --exclude-intervals excl_intervals.interval_list
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
198 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
199 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("bed")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
200 --exclude-intervals excl_intervals.bed
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
201 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
202 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("vcf")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
203 --exclude-intervals excl_intervals.vcf
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
204 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
205 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
206 #elif $getVar($sect + "excl_ival_type.excl_ival_type_sel") == "excl_ival_text"
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
207 #if $varExists($sect + "excl_ival_type.exclude_intervals")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
208 --exclude-intervals $getVar($sect + "excl_ival_type.exclude_intervals")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
209 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
210 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
211 #pass
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
212 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
213 #if $varExists($sect + "excl_ival_type.interval_exclusion_padding")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
214 --interval-exclusion-padding $getVar($sect + "excl_ival_type.interval_exclusion_padding")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
215 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
216 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
217 #end for
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
218 </template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
219
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
220 <template name="pre_gatk_excl_ints_chth"><![CDATA[
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
221 #for $sect in $sections
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
222 #if $varExists($sect + "excl_ival_type.excl_ival_type_sel")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
223 #if $getVar($sect + "excl_ival_type.excl_ival_type_sel") == "excl_ival_file"
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
224 #if $varExists($sect + "excl_ival_type.exclude_intervals")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
225 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("gatk_interval")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
226 ln -s $getVar($sect + "excl_ival_type.exclude_intervals") excl_intervals.interval_list &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
227 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
228 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("bed")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
229 ln -s $getVar($sect + "excl_ival_type.exclude_intervals") excl_intervals.bed &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
230 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
231 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("vcf")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
232 ln -s $getVar($sect + "excl_ival_type.exclude_intervals") excl_intervals.vcf &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
233 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
234 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
235 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
236 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
237 #end for
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
238 ]]></template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
239
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
240 <!--Sequence dictionary selection options for Picard type tools-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
241 <template name="picard_seqdict_opts">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
242 #for $sect in $sections
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
243 #if $varExists($sect + "seqdict_source.seqdict_source_selector")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
244 #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "no_seq_dict"
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
245 #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "history"
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
246 #set seq_dict_loc = ''.join($getVar($sect + seqdict_source.seqdict_sequence).fields.path.split('.')[:-1]) + '.dict'
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
247 --SEQUENCE_DICTIONARY $seq_dict_loc
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
248 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
249 --SEQUENCE_DICTIONARY $getVar($sect + "seqdict_source.seqdict_sequence")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
250 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
251 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
252 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
253 #end for
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
254 </template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
255
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
256 <template name="gatk_seqdict">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
257 #for $sect in $sections
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
258 #if $varExists($sect + "seqdict_source.seqdict_source_selector")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
259 #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "no_seq_dict"
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
260 #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "history"
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
261 #set $seq_dict_loc = ''.join($getVar($sect + "seqdict_source.seqdict_sequence").fields.path.split('.')[:-1]) + '.dict'
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
262 --sequence-dictionary $seq_dict_loc
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
263 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
264 --sequence-dictionary $getVar($sect + "seqdict_source.seqdict_sequence")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
265 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
266 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
267 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
268 #end for
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
269 </template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
270
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
271 <xml name="seq_dict_sel">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
272 <conditional name="seqdict_source">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
273 <param name="seqdict_source_selector" type="select" label="Choose the source for the sequence dictionary">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
274 <option value="cached">Locally cached</option>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
275 <option value="history">History</option>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
276 <option value="no_seq_dict" selected="true">Do not pass</option>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
277 </param>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
278 <when value="cached">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
279 <param name="seqdict_sequence" type="select" label="Sequence Dictionary" help="Sequence dictionary file." >
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
280 <options from_data_table="all_fasta" >
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
281 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
282 </options>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
283 </param>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
284 </when>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
285 <when value="history">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
286 <param name="seqdict_sequence" type="data" format="txt" label="Sequence Dictionary" help="Sequence dictionary file. Must be in dict format." />
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
287 </when>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
288 <when value="no_seq_dict" />
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
289 </conditional>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
290 </xml>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
291
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
292 <!--BAM input-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
293 <template name="picard_tumor_bam_input">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
294 --INPUT tumor.bam
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
295 </template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
296
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
297 <template name="gatk_tumor_bam_input">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
298 --input tumor.bam
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
299 </template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
300
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
301 <template name="tumor_bam_index_pre_chth"><![CDATA[
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
302 #for $sect in $sections
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
303 #if $varExists($sect + "tumor")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
304 #if $getVar($sect + "tumor").is_of_type("bam")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
305 ln -s $getVar($sect + "tumor") tumor.bam &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
306 samtools index tumor.bam &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
307 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
308 ln -s $getVar($sect + "tumor") tumor.sam &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
309 samtools view -bS tumor.sam -o tumor.bam &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
310 samtools index tumor.bam &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
311 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
312 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
313 #end for
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
314 ]]></template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
315
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
316 <xml name="gatk_tumor_bam_req_params">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
317 <param name="tumor" argument="--tumor" type="data" format="bam,sam" label="Input Tumor BAM/SAM/CRAM file" />
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
318 </xml>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
319
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
320 <template name="picard_tumor_bam_index"><![CDATA[
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
321 #if $tumor.is_of_type("bam")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
322 ln -s $INPUT tumor.bam &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
323 samtools index tumor.bam &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
324 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
325 ln -s $INPUT tumor.sam &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
326 samtools view -bS tumor.sam -o tumor.bam &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
327 samtools index tumor.bam &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
328 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
329 ]]></template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
330
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
331 <template name="picard_normal_bam_input">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
332 --INPUT normal.bam
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
333 </template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
334
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
335 <template name="gatk_normal_bam_input">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
336 --input normal.bam
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
337 </template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
338
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
339 <template name="normal_bam_index_pre_chth"><![CDATA[
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
340 #for $sect in $sections
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
341 #if $varExists($sect + "normal")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
342 #if $getVar($sect + "normal").is_of_type("bam")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
343 ln -s $getVar($sect + "normal") normal.bam &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
344 samtools index normal.bam &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
345 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
346 ln -s $getVar($sect + "normal") normal.sam &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
347 samtools view -bS normal.sam -o normal.bam &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
348 samtools index normal.bam &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
349 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
350 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
351 #end for
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
352 ]]></template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
353
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
354 <xml name="gatk_normal_bam_req_params">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
355 <param name="normal" argument="--normal" type="data" format="bam,sam" label="Input Tumor BAM/SAM/CRAM file" />
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
356 </xml>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
357
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
358 <template name="picard_normal_bam_index"><![CDATA[
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
359 #if $normal.is_of_type("bam")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
360 ln -s $INPUT normal.bam &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
361 samtools index normal.bam &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
362 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
363 ln -s $INPUT normal.sam &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
364 samtools view -bS normal.sam -o normal.bam &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
365 samtools index normal.bam &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
366 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
367 ]]></template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
368
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
369 <!--Output goes to stdout, no output parameter exists.-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
370 <template name="stdout_to_output">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
371 > output.txt
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
372 </template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
373
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
374 <xml name="stdout_to_output_params">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
375 <data format="txt" name="output" label="${tool.name} on ${on_string}: txt" from_work_dir="output.txt" />
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
376 </xml>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
377
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
378 <!--Multiple input files, true for List[File] types, and sometimes List[String] types -->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
379 <template name="gatk_input_multi"><![CDATA[
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
380 #for $num, $file in enumerate($variant)
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
381 #if $file.is_of_type("vcf_bgzip")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
382 --variant input${num}.vcf.gz
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
383 #elif $file.is_of_type("txt")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
384 --variant input${num}.list
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
385 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
386 --variant input${num}.vcf
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
387 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
388 #end for
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
389 ]]></template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
390
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
391 <!--Multiple input files, true for List[File] types, and sometimes List[String] types -->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
392 <template name="gatk_input_single"><![CDATA[
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
393 #if $variant.is_of_type("vcf_bgzip")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
394 --variant input${num}.vcf.gz
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
395 #elif $variant.is_of_type("txt")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
396 --variant input${num}.list
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
397 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
398 --variant input${num}.vcf
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
399 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
400 ]]></template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
401
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
402 <template name="gatk_tabix_multi"><![CDATA[
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
403 #for $num, $file in enumerate($variant)
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
404 #set datatype = $file.datatype
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
405 #if $file.is_of_type("vcf_bgzip")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
406 ln -s $file input${num}.vcf.gz &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
407 tabix input${num}.vcf.gz &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
408 #elif $file.is_of_type("txt")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
409 ln -s $file input${num}.list &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
410 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
411 ln -s $file input${num}.vcf &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
412 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
413 #end for
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
414 ]]></template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
415
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
416 <xml name="vcf_input_params_multi">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
417 <param name="input" type="data" multiple="true" format="vcf,vcf_bgzip" label="Input VCF file" help="Input VCF(s) to be sorted. Multiple inputs must have the same sample names (in order)"/>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
418 </xml>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
419
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
420
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
421
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
422 <!--ABOVE HAS BEEN REVIEWED-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
423
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
424
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
425
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
426
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
427
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
428
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
429
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
430
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
431
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
432
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
433 <!--{-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
434 <!--"summary": "BAM/SAM/CRAM file containing reads",-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
435 <!--"name": "&#45;&#45;input",-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
436 <!--"synonyms": "-I",-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
437 <!--"type": "List[String]",-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
438 <!--"required": "yes",-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
439 <!--"fulltext": "",-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
440 <!--"defaultValue": "[]",-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
441 <!--"minValue": "NA",-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
442 <!--"maxValue": "NA",-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
443 <!--"minRecValue": "NA",-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
444 <!--"maxRecValue": "NA",-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
445 <!--"kind": "required",-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
446 <!--"options": []-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
447 <!--},-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
448 <!--Required BAM input, GATK tool, may be specified multiple times.-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
449 <!--BAM should be indexed on the fly.-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
450 <!--Parameter is required, so is not contained within a section.-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
451 <!--Only decriptor that makes this unique for all input parameters is the summary field.-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
452 <!--{'pre_chth': ['bam_index_pre_chth'],-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
453 <!--'main_chth': ['picard_bam_input'],-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
454 <!--'main_xml': ['gatk_bam_req_params']}},-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
455
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
456
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
457
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
458
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
459
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
460
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
461
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
462
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
463
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
464
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
465
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
466
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
467
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
468 <!--Macros for multiple input tools. List[File] in GATK json.-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
469 <template name="vcf_tabix_multi"><![CDATA[
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
470 #for $num, $file in enumerate($input)
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
471 #set datatype = $file.datatype
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
472 #if $file.is_of_type("vcf_bgzip")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
473 ln -s $file input${num}.vcf.gz &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
474 tabix input${num}.vcf.gz &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
475 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
476 ln -s $file input${num}.vcf &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
477 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
478 #end for
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
479 ]]></template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
480
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
481 <template name="vcf_input_multi_picard"><![CDATA[
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
482 #for $num, $file in enumerate($input)
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
483 #if $file.is_of_type("vcf_bgzip")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
484 --INPUT input${num}.vcf.gz
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
485 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
486 --INPUT input${num}.vcf
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
487 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
488 #end for
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
489 ]]></template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
490
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
491 <template name="vcf_input_multi"><![CDATA[
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
492 #for $num, $file in enumerate($input)
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
493 #if $file.is_of_type("vcf_bgzip")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
494 --input input${num}.vcf.gz
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
495 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
496 --input input${num}.vcf
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
497 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
498 #end for
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
499 ]]></template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
500
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
501
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
502 <!--Picard single input tools-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
503 <template name="vcf_tabix"><![CDATA[
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
504 #set datatype = $input.datatype
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
505 #if $input.is_of_type("vcf_bgzip")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
506 ln -s $input input.vcf.gz &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
507 tabix input.vcf.gz &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
508 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
509 ln -s $input input.vcf &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
510 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
511 ]]></template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
512
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
513 <template name="gatk_tabix"><![CDATA[
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
514 #set datatype = $variant.datatype
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
515 #if $variant.is_of_type("vcf_bgzip")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
516 ln -s $variant input.vcf.gz &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
517 tabix input.vcf.gz &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
518 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
519 ln -s $variant input.vcf &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
520 gatk IndexFeatureFile -F input.vcf &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
521 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
522 ]]></template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
523
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
524 <template name="vcf_input_picard"><![CDATA[
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
525 #if $input.is_of_type("vcf_bgzip")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
526 --INPUT input.vcf.gz
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
527 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
528 --INPUT input.vcf
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
529 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
530 ]]></template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
531
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
532 <template name="vcf_input"><![CDATA[
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
533 #if $input.is_of_type("vcf_bgzip")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
534 --input input.vcf.gz
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
535 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
536 --input input.vcf
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
537 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
538 ]]></template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
539
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
540 <template name="gatk_input"><![CDATA[
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
541 #if $variant.is_of_type("vcf_bgzip")
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
542 --variant input.vcf.gz
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
543 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
544 --variant input.vcf
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
545 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
546 ]]></template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
547
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
548 <template name="gatk_gvcf_tabix"><![CDATA[
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
549 #if $variant
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
550 ln -s $variant input.g.vcf &&
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
551 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
552 ]]></template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
553
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
554 <template name="gatk_gvcf_input"><![CDATA[
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
555 --variant input.g.vcf
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
556 ]]></template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
557
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
558 <xml name="gatk_gvcf_input_params">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
559 <param name="variant" type="data" multiple="false" format="vcf" label="Input gVCF file" help=""/>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
560 </xml>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
561
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
562 <xml name="vcf_input_params">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
563 <param name="input" type="data" multiple="false" format="vcf,vcf_bgzip" label="Input VCF file" help="Input VCF(s) to be sorted. Multiple inputs must have the same sample names (in order)"/>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
564 </xml>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
565
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
566 <xml name="gatk_vcf_input_params">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
567 <param name="variant" type="data" multiple="false" format="vcf,vcf_bgzip" label="Input VCF file" help="A VCF file containing variants."/>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
568 </xml>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
569
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
570 <xml name="gatk_vcf_input_params_multi">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
571 <param name="variant" type="data" multiple="true" format="vcf,vcf_bgzip,txt" label="Input VCF file(s)" help="A VCF file containing variants or a list of VCFs. Can be specified multiple times."/>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
572 </xml>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
573
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
574 <xml name="gatk_req_params">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
575 <param name="input" type="data" format="bam,sam,cram" label="Input BAM/SAM/CRAM file" />
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
576 </xml>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
577
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
578 <!--HDF5 Inputs-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
579
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
580 <xml name="hdf5_input">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
581 <param name="input" type="data" format="h5,tabular" label="Input TSV or HDF5" help="Input TSV or HDF5 file containing integer read counts in genomic intervals for a single case sample (output of CollectReadCounts)." />
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
582 </xml>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
583
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
584 <template name="hdf5_input_chth"><![CDATA[
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
585 --input "${input}"
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
586 ]]></template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
587
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
588 <template name="hdf5_output_chth">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
589 --output "${output}"
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
590 </template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
591
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
592 <xml name="hdf5_output">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
593 <data format="h5" name="output" label="${tool.name} on ${on_string}: HDF5" help="Output file for read counts." />
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
594 </xml>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
595
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
596 <!--Output specific to ModelSegments. Files created based on prefix, so force that to be what we want, then pull important files with from_work_dir.-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
597 <!--${SAMPLE}.cr.seg-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
598 <!--${SAMPLE}.modelFinal.seg-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
599 <template name="modelsegments_chth"><![CDATA[
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
600 --output "."
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
601 --output-prefix "modelsegments"
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
602 ]]></template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
603
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
604 <xml name="modelsegments_output">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
605 <data format="tabular" name="cr_seg" label="${tool.name} on ${on_string}: cr.seg" help="Copy-ratio segments." from_work_dir="modelsegments.cr.seg"/>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
606 <data format="tabular" name="modelfinal_seg" label="${tool.name} on ${on_string}: modelFinal.seg" help="Modeled Segments" from_work_dir="modelsegments.modelFinal.seg"/>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
607 </xml>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
608
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
609 <!--deltaMAD.txt-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
610 <!--denoisedLimit4.png-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
611 <!--denoisedMAD.txt-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
612 <!--denoised.png-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
613 <!--scaledDeltaMAD.txt-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
614 <!--modeled.png-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
615 <!--standardizedMAD.txt-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
616
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
617 <template name="plotmodeledsegments_chth"><![CDATA[
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
618 --output "."
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
619 --output-prefix "plotmodeledsegments"
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
620 ]]></template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
621
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
622 <xml name="plotmodeledsegments_output">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
623 <data format="png" name="modeled_png" label="${tool.name} on ${on_string}: modeled.png" help="Copy-Ratio Plot" from_work_dir="plotmodeledsegments.modeled.png"/>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
624 </xml>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
625
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
626 <!--Common Picard options-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
627 <template name="picard_opts">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
628 #if $picard_adv.arguments_file
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
629 --arguments_file ${picard_adv.arguments_file}
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
630 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
631 --COMPRESSION_LEVEL ${picard_adv.COMPRESSION_LEVEL}
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
632 #if $picard_adv.GA4GH_CLIENT_SECRETS
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
633 --GA4GH_CLIENT_SECRETS ${picard_adv.GA4GH_CLIENT_SECRETS}
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
634 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
635 --MAX_RECORDS_IN_RAM ${picard_adv.MAX_RECORDS_IN_RAM}
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
636 --VALIDATION_STRINGENCY ${picard_adv.VALIDATION_STRINGENCY}
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
637 --VERBOSITY ${picard_adv.VERBOSITY}
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
638 ${picard_adv.CREATE_MD5_FILE}
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
639 ${picard_adv.USE_JDK_DEFLATER}
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
640 ${picard_adv.USE_JDK_INFLATER}
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
641 </template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
642
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
643 <xml name="picard_params">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
644 <section name="picard_adv" title="Advanced Picard Options (Only change these if you know what you're doing.)" expanded="False">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
645 <param argument="--arguments_file" type="data" optional="true" format="txt" label="Arguments File" help="read one or more arguments files and add them to the command line" />
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
646 <param argument="--COMPRESSION_LEVEL" type="integer" optional="true" value="5" min="1" max="9" label="Compression Level" help="Compression level for all compressed files created (e.g. BAM and VCF)." />
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
647 <param argument="--CREATE_MD5_FILE" truevalue="--CREATE_MD5_FILE" falsevalue="" type="boolean" optional="true" checked="false" label="Create MD5 File" help="Whether to create an MD5 digest for any BAM or FASTQ files created." />
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
648 <param argument="--GA4GH_CLIENT_SECRETS" type="data" format="json" optional="true" label="Ga4Gh Client Secrets" help="Google Genomics API client_secrets.json file path." />
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
649 <param argument="--MAX_RECORDS_IN_RAM" type="integer" optional="true" value="500000" label="Max Records In Ram" help="When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed." />
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
650 <param argument="--TMP_DIR" type="text" optional="true" label="Tmp Dir" help="One or more directories with space available to be used by this program for temporary storage of working files. Keep in mind, you must be able to access this directory from either your user, or from the Galaxy user, depending on your configuration." />
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
651 <param argument="--USE_JDK_DEFLATER" truevalue="--USE_JDK_DEFLATER" falsevalue="" type="boolean" optional="true" checked="false" label="Use Jdk Deflater" help="Use the JDK Deflater instead of the Intel Deflater for writing compressed output" />
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
652 <param argument="--USE_JDK_INFLATER" truevalue="--USE_JDK_INFLATER" falsevalue="" type="boolean" optional="true" checked="false" label="Use Jdk Inflater" help="Use the JDK Inflater instead of the Intel Inflater for reading compressed input" />
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
653 <param argument="--VALIDATION_STRINGENCY" type="select" optional="true" label="Validation Stringency" help="Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded." >
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
654 <option value="STRICT" selected="true">STRICT</option>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
655 <option value="LENIENT" selected="false">LENIENT</option>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
656 <option value="SILENT" selected="false">SILENT</option>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
657 </param>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
658 <param argument="--VERBOSITY" type="select" optional="true" label="Verbosity" help="Control verbosity of logging." >
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
659 <option value="ERROR" selected="false">ERROR</option>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
660 <option value="WARNING" selected="false">WARNING</option>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
661 <option value="INFO" selected="true">INFO</option>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
662 <option value="DEBUG" selected="false">DEBUG</option>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
663 </param>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
664 </section>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
665 </xml>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
666
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
667 <!--Provides option to create gzipped output for VCF files-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
668 <xml name="gzip_vcf_params">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
669 <param name="gzipped_output" type="boolean" checked="true" label="GZIP Output?" help="If you would like gzipped output, check this box. In general, it would be preferable to do this, unless your downstream tool does not support handling of gzipped files." />
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
670 </xml>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
671
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
672 <!--Output related Picard options-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
673 <xml name="gzip_vcf_output_params">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
674 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string}: vcf" from_work_dir="output.vcf" >
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
675 <filter>not gzipped_output</filter>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
676 </data>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
677 <data format="vcf_bgzip" name="output_vcf_bgzip" label="${tool.name} on ${on_string}: vcf_bgzip" from_work_dir="output.vcf.gz" >
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
678 <filter>gzipped_output</filter>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
679 </data>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
680 </xml>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
681
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
682
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
683 <!--These are the same, other than the capitalization of output, so maybe a better way to do this.-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
684 <template name="picard_vcf_output_opts">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
685 #if $gzipped_output
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
686 --OUTPUT output.vcf.gz
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
687 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
688 --OUTPUT output.vcf
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
689 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
690 </template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
691
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
692 <template name="vcf_output_opts">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
693 #if $gzipped_output
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
694 --output output.vcf.gz
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
695 #else
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
696 --output output.vcf
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
697 #end if
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
698 </template>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
699
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
700 <xml name="picard_output_params">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
701 <data format="txt" name="output_md5" label="${tool.name} on ${on_string}: md5sum(txt)" from_work_dir="output.bam.md5" >
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
702 <filter>picard_adv['CREATE_MD5_FILE']</filter>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
703 </data>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
704 </xml>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
705
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
706
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
707 <!--<template name="ref_opts">-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
708 <!--#set $sections = ['optional','advanced','deprecated','']-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
709 <!--#silent $sys.stderr.write("I WOULD LIKE TO SHOW THE SECTION VARIABLE: '${sections}'\n")-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
710 <!--#for $sect in $sections-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
711 <!--#if $varExists('$sect.reference_source.reference_source_selector')-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
712 <!--#if $sect.reference_source.reference_source_selector != "no_ref"-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
713 <!--#if $sect.reference_source.reference_source_selector != "history"-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
714 <!--&#45;&#45;reference ${sect.reference_source.reference_sequence.fields.path}-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
715 <!--#else-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
716 <!--&#45;&#45;reference ${sect.reference_source.reference_sequence}-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
717 <!--#end if-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
718 <!--#end if-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
719 <!--#end if-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
720 <!--#end for-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
721 <!--</template>-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
722
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
723
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
724 <!--<template name="ref_opts_opt">-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
725 <!--#if $optional.reference_source.reference_source_selector != "no_ref"-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
726 <!--#if $optional.reference_source.reference_source_selector != "history"-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
727 <!--&#45;&#45;reference ${optional.reference_source.reference_sequence.fields.path}-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
728 <!--#else-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
729 <!--&#45;&#45;reference ${optional.reference_source.reference_sequence}-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
730 <!--#end if-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
731 <!--#end if-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
732 <!--</template>-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
733
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
734
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
735 <!--Citations-->
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
736 <xml name="citations">
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
737 <citation type="doi">10.1101/gr.107524.110</citation>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
738 <citation type="doi">10.1038/ng.806</citation>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
739 <citation type="doi">10.1002/0471250953.bi1110s43</citation>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
740 <citation type="doi">10.1101/201178</citation>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
741 <yield />
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
742 </xml>
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
743
504de035ac0f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
artbio
parents:
diff changeset
744 </macros>