annotate vcfs2fasta.xml @ 1:162c88041ed7 draft

Uploaded
author ulfschaefer
date Tue, 10 May 2016 05:16:08 -0400
parents cb29f95c7b88
children 2cb7b6e42f72
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
1 <tool id="vcfs2fasta" name="VCFs to fasta" version="1.0">
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
2 <description>Takes a set of VCF files and outputs a multi fasta file with only the variant positions.</description>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
3 <requirements>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
4 <requirement type="package" version="2.7.10">python</requirement>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
5 <requirement type="package" version="0.6.8dev">pyvcf</requirement>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
6 <requirement type="package" version="3.11">pyyaml</requirement>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
7 <requirement type="package" version="2.0.2">bintrees</requirement>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
8 <requirement type="package" version="1.66">biopython</requirement>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
9 <requirement type="package" version="1.4">matplotlib</requirement>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
10 <requirement type="package" version="0.23.1">cython</requirement>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
11 <requirement type="package" version="1.0">phephenix</requirement>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
12 </requirements>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
13 <stdio>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
14 <!-- Assume anything other than zero is an error -->
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
15 <exit_code range="1:" />
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
16 <exit_code range=":-1" />
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
17 </stdio>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
18 <command interpreter="bash">
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
19 vcfs2fasta.sh
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
20 $output
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
21 #if str($mix_cond.mix) == "yes":
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
22 $mix_cond.mix_value
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
23 #else
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
24 NOTTHERE
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
25 #end if
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
26 #if str($cols_cond.cols) == "yes":
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
27 $cols_cond.column_ns
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
28 #else
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
29 NOTTHERE
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
30 #end if
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
31 #if str($sample_cond.sample) == "yes":
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
32 $sample_cond.sample_ns
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
33 #else
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
34 NOTTHERE
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
35 #end if
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
36 #if str($reference_cond.reference) == "yes":
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
37 $reference_cond.ref_fa
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
38 #else
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
39 NOTTHERE
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
40 #end if
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
41 #if str($include_cond.include) == "yes":
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
42 $include_cond.in_bed
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
43 #else
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
44 NOTTHERE
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
45 #end if
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
46 #if str($exclude_cond.exclude) == "yes":
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
47 $exclude_cond.ex_bed
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
48 #else
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
49 NOTTHERE
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
50 #end if
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
51 #for $i, $input_vcf in enumerate( $input_vcfs ):
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
52 "${input_vcf}"
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
53 #end for
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
54 </command>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
55
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
56 <inputs>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
57 <param name="input_vcfs" type="data" multiple="true" format="vcf" label="Input VCF file(s)" />
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
58 <conditional name="mix_cond">
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
59 <param name="mix" type="select" label="With Mixtures" help="Specify this option with a threshold to output mixtures above this threshold.">
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
60 <option value="yes">Specify</option>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
61 <option value="no" selected="true">Do not specify</option>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
62 </param>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
63 <when value="yes">
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
64 <param name="mix_value" type="float" value="0.5" label="Mixture value" />
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
65 </when>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
66 </conditional>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
67 <conditional name="cols_cond">
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
68 <param name="cols" type="select" label="Column Ns" help="Keeps columns with fraction of Ns above specified threshold.">
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
69 <option value="yes">Specify</option>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
70 <option value="no" selected="true">Do not specify</option>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
71 </param>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
72 <when value="yes">
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
73 <param name="column_ns" type="float" value="0.5" label="Column Ns value" />
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
74 </when>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
75 </conditional>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
76 <conditional name="sample_cond">
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
77 <param name="sample" type="select" label="Sample Ns" help="Keeps samples with fraction of Ns above specified threshold.">
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
78 <option value="yes">Specify</option>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
79 <option value="no" selected="true">Do not specify</option>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
80 </param>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
81 <when value="yes">
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
82 <param name="sample_ns" type="float" value="0.5" label="Sample Ns value" />
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
83 </when>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
84 </conditional>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
85 <conditional name="reference_cond">
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
86 <param name="reference" type="select" label="Reference genome file" help="If path to reference specified, then whole genome will be outputted.">
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
87 <option value="yes">Specify</option>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
88 <option value="no" selected="true">Do not specify</option>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
89 </param>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
90 <when value="yes">
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
91 <param name="ref_fa" type="data" format="fasta" label="Reference fasta file" help="Fasta format"/>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
92 </when>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
93 </conditional>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
94 <conditional name="include_cond">
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
95 <param name="include" type="select" label="Include region" help="Specify regions to include in a bed file.">
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
96 <option value="yes">Specify</option>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
97 <option value="no" selected="true">Do not specify</option>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
98 </param>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
99 <when value="yes">
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
100 <param name="in_bed" type="data" format="bed" label="Include regions bed file" help="bed format"/>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
101 </when>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
102 </conditional>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
103 <conditional name="exclude_cond">
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
104 <param name="exclude" type="select" label="Exclude region" help="Specify regions to exclude in a bed file.">
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
105 <option value="yes">Specify</option>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
106 <option value="no" selected="true">Do not specify</option>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
107 </param>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
108 <when value="yes">
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
109 <param name="ex_bed" type="data" format="bed" label="Exclude regions bed file" help="bed format"/>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
110 </when>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
111 </conditional>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
112 </inputs>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
113
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
114 <outputs>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
115 <data format="fasta" name="output" label="${tool.name} on ${on_string}: FASTA file" />
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
116 </outputs>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
117 <test>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
118 <param name="input_vcfs" value="1_short.vcf" ftype="vcf" />
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
119 <param name="input_vcfs" value="2_short.vcf" ftype="vcf" />
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
120 <output name="output" file="testresult.fa" ftype="fasta" />
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
121 </test>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
122 <help>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
123
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
124 </help>
cb29f95c7b88 Uploaded
ulfschaefer
parents:
diff changeset
125 </tool>