Mercurial > repos > ulfschaefer > phephenix
comparison vcfs2fasta.xml @ 0:cb29f95c7b88 draft
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author | ulfschaefer |
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date | Mon, 09 May 2016 09:27:06 -0400 |
parents | |
children | 2cb7b6e42f72 |
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-1:000000000000 | 0:cb29f95c7b88 |
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1 <tool id="vcfs2fasta" name="VCFs to fasta" version="1.0"> | |
2 <description>Takes a set of VCF files and outputs a multi fasta file with only the variant positions.</description> | |
3 <requirements> | |
4 <requirement type="package" version="2.7.10">python</requirement> | |
5 <requirement type="package" version="0.6.8dev">pyvcf</requirement> | |
6 <requirement type="package" version="3.11">pyyaml</requirement> | |
7 <requirement type="package" version="2.0.2">bintrees</requirement> | |
8 <requirement type="package" version="1.66">biopython</requirement> | |
9 <requirement type="package" version="1.4">matplotlib</requirement> | |
10 <requirement type="package" version="0.23.1">cython</requirement> | |
11 <requirement type="package" version="1.0">phephenix</requirement> | |
12 </requirements> | |
13 <stdio> | |
14 <!-- Assume anything other than zero is an error --> | |
15 <exit_code range="1:" /> | |
16 <exit_code range=":-1" /> | |
17 </stdio> | |
18 <command interpreter="bash"> | |
19 vcfs2fasta.sh | |
20 $output | |
21 #if str($mix_cond.mix) == "yes": | |
22 $mix_cond.mix_value | |
23 #else | |
24 NOTTHERE | |
25 #end if | |
26 #if str($cols_cond.cols) == "yes": | |
27 $cols_cond.column_ns | |
28 #else | |
29 NOTTHERE | |
30 #end if | |
31 #if str($sample_cond.sample) == "yes": | |
32 $sample_cond.sample_ns | |
33 #else | |
34 NOTTHERE | |
35 #end if | |
36 #if str($reference_cond.reference) == "yes": | |
37 $reference_cond.ref_fa | |
38 #else | |
39 NOTTHERE | |
40 #end if | |
41 #if str($include_cond.include) == "yes": | |
42 $include_cond.in_bed | |
43 #else | |
44 NOTTHERE | |
45 #end if | |
46 #if str($exclude_cond.exclude) == "yes": | |
47 $exclude_cond.ex_bed | |
48 #else | |
49 NOTTHERE | |
50 #end if | |
51 #for $i, $input_vcf in enumerate( $input_vcfs ): | |
52 "${input_vcf}" | |
53 #end for | |
54 </command> | |
55 | |
56 <inputs> | |
57 <param name="input_vcfs" type="data" multiple="true" format="vcf" label="Input VCF file(s)" /> | |
58 <conditional name="mix_cond"> | |
59 <param name="mix" type="select" label="With Mixtures" help="Specify this option with a threshold to output mixtures above this threshold."> | |
60 <option value="yes">Specify</option> | |
61 <option value="no" selected="true">Do not specify</option> | |
62 </param> | |
63 <when value="yes"> | |
64 <param name="mix_value" type="float" value="0.5" label="Mixture value" /> | |
65 </when> | |
66 </conditional> | |
67 <conditional name="cols_cond"> | |
68 <param name="cols" type="select" label="Column Ns" help="Keeps columns with fraction of Ns above specified threshold."> | |
69 <option value="yes">Specify</option> | |
70 <option value="no" selected="true">Do not specify</option> | |
71 </param> | |
72 <when value="yes"> | |
73 <param name="column_ns" type="float" value="0.5" label="Column Ns value" /> | |
74 </when> | |
75 </conditional> | |
76 <conditional name="sample_cond"> | |
77 <param name="sample" type="select" label="Sample Ns" help="Keeps samples with fraction of Ns above specified threshold."> | |
78 <option value="yes">Specify</option> | |
79 <option value="no" selected="true">Do not specify</option> | |
80 </param> | |
81 <when value="yes"> | |
82 <param name="sample_ns" type="float" value="0.5" label="Sample Ns value" /> | |
83 </when> | |
84 </conditional> | |
85 <conditional name="reference_cond"> | |
86 <param name="reference" type="select" label="Reference genome file" help="If path to reference specified, then whole genome will be outputted."> | |
87 <option value="yes">Specify</option> | |
88 <option value="no" selected="true">Do not specify</option> | |
89 </param> | |
90 <when value="yes"> | |
91 <param name="ref_fa" type="data" format="fasta" label="Reference fasta file" help="Fasta format"/> | |
92 </when> | |
93 </conditional> | |
94 <conditional name="include_cond"> | |
95 <param name="include" type="select" label="Include region" help="Specify regions to include in a bed file."> | |
96 <option value="yes">Specify</option> | |
97 <option value="no" selected="true">Do not specify</option> | |
98 </param> | |
99 <when value="yes"> | |
100 <param name="in_bed" type="data" format="bed" label="Include regions bed file" help="bed format"/> | |
101 </when> | |
102 </conditional> | |
103 <conditional name="exclude_cond"> | |
104 <param name="exclude" type="select" label="Exclude region" help="Specify regions to exclude in a bed file."> | |
105 <option value="yes">Specify</option> | |
106 <option value="no" selected="true">Do not specify</option> | |
107 </param> | |
108 <when value="yes"> | |
109 <param name="ex_bed" type="data" format="bed" label="Exclude regions bed file" help="bed format"/> | |
110 </when> | |
111 </conditional> | |
112 </inputs> | |
113 | |
114 <outputs> | |
115 <data format="fasta" name="output" label="${tool.name} on ${on_string}: FASTA file" /> | |
116 </outputs> | |
117 <test> | |
118 <param name="input_vcfs" value="1_short.vcf" ftype="vcf" /> | |
119 <param name="input_vcfs" value="2_short.vcf" ftype="vcf" /> | |
120 <output name="output" file="testresult.fa" ftype="fasta" /> | |
121 </test> | |
122 <help> | |
123 | |
124 </help> | |
125 </tool> |