Mercurial > repos > iuc > medaka_variant

annotate variant.xml @ 6:103a681e82a1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
author iuc
date Wed, 10 Feb 2021 08:25:36 +0000
parents 294565bd47cd
children 103c8b06c95f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
6
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
2 <tool id="medaka_variant" name="medaka variant tool" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@">
0
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
3 <description>Probability decoding</description>
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
4 <macros>
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
5 <import>macros.xml</import>
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
6 </macros>
4
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
7 <expand macro="requirements">
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
8 <requirement type="package" version="1.4.1">scipy</requirement>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
9 </expand>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
10
0
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
11 <expand macro="version_command"/>
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
12 <command detect_errors="exit_code"><![CDATA[
1
740e5a738658 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
iuc
parents: 0
diff changeset
13 ## initialize
740e5a738658 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
iuc
parents: 0
diff changeset
14 @REF_FASTA@
0
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
15
4
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
16
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
17 #if $pool.pool_mode == "Yes":
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
18 ## run
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
19 medaka variant
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
20 ## optional
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
21 --debug
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
22 #if $regions
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
23 --regions '${regions}'
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
24 #end if
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
25 $verbose
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
26 ## required
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
27 reference.fa
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
28 #for $current in $pool.inputs
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
29 '$current'
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
30 #end for
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
31 '$out_result' ## output
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
32
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
33 2>&1 | tee '$out_log'
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
34 #elif $pool.pool_mode == "No":
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
35 ## run
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
36 medaka variant
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
37 ## optional
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
38 --debug
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
39 #if $regions
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
40 --regions '${regions}'
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
41 #end if
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
42 $verbose
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
43 ## required
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
44 reference.fa
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
45 '$pool.input'
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
46 '$out_result' ##output
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
47 2>&1 | tee '$out_log'
1
740e5a738658 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
iuc
parents: 0
diff changeset
48 #end if
3
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
49
6
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
50 #if $out_annotated:
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
51 && ln -s '$output_annotated.in_bam' in.bam
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
52 && ln -s '$output_annotated.in_bam.metadata.bam_index' in.bai
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
53 && medaka tools annotate --pad $output_annotated.pad '$out_result' reference.fa in.bam tmp.vcf
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
54 && '$__tool_directory__/convert_VCF_info_fields.py' tmp.vcf '$out_annotated'
3
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
55 #end if
1
740e5a738658 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
iuc
parents: 0
diff changeset
56 ]]></command>
0
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
57 <inputs>
4
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
58 <conditional name="pool">
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
59 <param name="pool_mode" type="select" label="Are you pooling HDF5 datasets?">
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
60 <option value="No" selected="True">No</option>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
61 <option value="Yes">Yes</option>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
62 </param>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
63 <when value="Yes">
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
64 <param name="inputs" type="data" format="h5" multiple="true" label="Select consensus file(s)"/>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
65 </when>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
66 <when value="No">
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
67 <param name="input" type="data" format="h5" label="Select consensus file(s)"/>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
68 </when>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
69 </conditional>
0
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
70 <expand macro="reference"/>
4
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
71 <param argument="--regions" type="text" value="" optional="true" label="Set reference names to limit variant calling" help="Separated by ','.">
3
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
72 <sanitizer invalid_char="">
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
73 <valid initial="string.ascii_letters,string.digits">
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
74 <add value="_"/>
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
75 <add value=","/>
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
76 <add value="."/>
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
77 </valid>
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
78 </sanitizer>
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
79 </param>
0
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
80 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Populate VCF info fields?"/>
3
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
81 <conditional name="output_annotated">
4
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
82 <param name="output_annotated_select" type="select" label="Output annotated VCF?" help="Annotate allele frequency, depth of coverage, etc for each variant (requires BAM file)">
3
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
83 <option value="true" selected="true">Output annotated VCF</option>
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
84 <option value="false">Don't output annotated VCF</option>
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
85 </param>
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
86 <when value="true">
6
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
87 <param name="in_bam" type="data" format="bam" optional="false" label="BAM to annotate the VCF"/>
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
88 <param name="pad" type="integer" min="1" value="25" label="Padding width on either side of variant for realignment in medaka tools anntotate, used to calculate DPSP, DPSPS, AF, FAF, RAF, SB, DP4, and AS in the output annotated VCF"/>
3
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
89 </when>
4
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
90 <when value="false"/>
3
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
91 </conditional>
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
92 <param name="output_log_bool" type="boolean" label="Output log file?" checked="true"/>
0
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
93 </inputs>
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
94 <outputs>
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
95 <!-- standard -->
3
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
96 <data name="out_result" format="vcf" label="${tool.name} on ${on_string}: Result"/>
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
97 <!-- optional -->
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
98 <data name="out_annotated" format="vcf" label="${tool.name} on ${on_string}: Annotated">
6
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
99 <filter>output_annotated['output_annotated_select']!='false'</filter>
0
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
100 </data>
1
740e5a738658 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"
iuc
parents: 0
diff changeset
101 <data name="out_log" format="tabular" label="${tool.name} on ${on_string}: Log">
3
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
102 <filter>output_log_bool</filter>
0
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
103 </data>
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
104 </outputs>
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
105 <tests>
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
106 <!-- #1 default -->
3
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
107 <test expect_num_outputs="3">
4
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
108 <conditional name="pool">
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
109 <param name="pool_mode" value="Yes"/>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
110 <param name="inputs" value="medaka_test.hdf,medaka_test.hdf"/>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
111 </conditional>
0
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
112 <conditional name="reference_source">
3
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
113 <param name="reference_source_selector" value="history"/>
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
114 <param name="ref_file" value="ref.fasta"/>
0
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
115 </conditional>
3
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
116 <conditional name="output_annotated">
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
117 <param name="output_annotated_select" value="true"/>
4
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
118 <param name="in_bam" value="medaka_test.bam"/>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
119 </conditional>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
120 <param name="output_log_bool" value="true"/>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
121
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
122 <output name="out_result">
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
123 <assert_contents>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
124 <has_n_lines n="9"/>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
125 <has_line line="##fileformat=VCFv4.1" />
6
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
126 <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
4
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
127 </assert_contents>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
128 </output>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
129 <output name="out_annotated">
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
130 <assert_contents>
6
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
131 <has_n_lines n="22"/>
4
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
132 <has_line line="##fileformat=VCFv4.1" />
6
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
133 <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
134 <has_line_matching expression="##convert_VCF_info_fields=[0-9]+\.[0-9]+" />
4
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
135 </assert_contents>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
136 </output>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
137 <output name="out_log">
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
138 <assert_contents>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
139 <has_n_lines n="10" />
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
140 </assert_contents>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
141 </output>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
142 </test>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
143 <!--No pooling-->
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
144 <test expect_num_outputs="3">
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
145 <conditional name="pool">
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
146 <param name="pool_mode" value="No"/>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
147 <param name="input" value="medaka_test.hdf"/>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
148 </conditional>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
149 <conditional name="reference_source">
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
150 <param name="reference_source_selector" value="history"/>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
151 <param name="ref_file" value="ref.fasta"/>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
152 </conditional>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
153 <conditional name="output_annotated">
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
154 <param name="output_annotated_select" value="true"/>
43bc582c0556 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit c02f74da66f51b431b7cd8bd0d1cffde267e3332"
iuc
parents: 3
diff changeset
155 <param name="in_bam" value="medaka_test.bam"/>
3
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
156 </conditional>
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
157 <param name="output_log_bool" value="true"/>
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
158
0
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
159 <output name="out_result">
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
160 <assert_contents>
3
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
161 <has_n_lines n="9"/>
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
162 <has_line line="##fileformat=VCFv4.1" />
6
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
163 <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
0
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
164 </assert_contents>
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
165 </output>
3
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
166 <output name="out_annotated">
0
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
167 <assert_contents>
6
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
168 <has_n_lines n="22"/>
3
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
169 <has_line line="##fileformat=VCFv4.1" />
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
170 <has_line line="##medaka_version=1.0.3" />
6
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
171 <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
0
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
172 </assert_contents>
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
173 </output>
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
174 <output name="out_log">
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
175 <assert_contents>
3
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
176 <has_n_lines n="8" />
0
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
177 </assert_contents>
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
178 </output>
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
179 </test>
6
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
180 <!--No annotation or log-->
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
181 <test expect_num_outputs="1">
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
182 <conditional name="pool">
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
183 <param name="pool_mode" value="No"/>
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
184 <param name="input" value="medaka_test.hdf"/>
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
185 </conditional>
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
186 <conditional name="reference_source">
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
187 <param name="reference_source_selector" value="history"/>
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
188 <param name="ref_file" value="ref.fasta"/>
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
189 </conditional>
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
190 <conditional name="output_annotated">
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
191 <param name="output_annotated_select" value="false"/>
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
192 </conditional>
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
193 <param name="output_log_bool" value="false"/>
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
194
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
195 <output name="out_result">
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
196 <assert_contents>
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
197 <has_n_lines n="9"/>
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
198 <has_line line="##fileformat=VCFv4.1" />
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
199 <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
200 </assert_contents>
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
201 </output>
103a681e82a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 9b7d28ac59ad082874670ee989836631ba8d7fb4"
iuc
parents: 5
diff changeset
202 </test>
0
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
203 </tests>
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
204 <help><![CDATA[
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
205 .. class:: infomark
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
206
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
207 **What it does**
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
208
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
209 @WID@
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
210
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
211 The module *variant* decodes probabilities.
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
212
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
213 **Input**
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
214
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
215 - reference sequence (FASTA)
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
216 - (several) consensus files (H5/HDF)
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
217
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
218 **Output**
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
219
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
220 - decoded probabilities (VCF)
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
221
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
222 **References**
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
223
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
224 @REFERENCES@
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
225 ]]></help>
e6478a373449 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
iuc
parents:
diff changeset
226 <expand macro="citations"/>
3
009673c8ac31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"
iuc
parents: 1
diff changeset
227 </tool>