|
4
|
1 <tool id="affr2vcf" name="Convert Affymetrix" version="1.9">
|
|
|
2 <description>genotype calls and intensities to VCF</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="1.9">bcftools-gtc2vcf-plugin</requirement>
|
|
|
5 </requirements>
|
|
|
6 <command detect_errors="exit_code"><![CDATA[
|
|
|
7 #set text_outputs_dir = 'text_outputs'
|
|
|
8 mkdir $text_outputs_dir &&
|
|
|
9 bcftools +affy2vcf.so
|
|
|
10 -- fasta_ref '$fasta_ref'
|
|
|
11 --annot '$annot'
|
|
|
12 --snp-posteriors '$text_outputs_dir/snp_posteriors.txt'
|
|
|
13 --summary '$text_outputs_dir/summary.txt'
|
|
|
14 --report '$text_outputs_dir/report.txt'
|
|
|
15 --calls '$text_outputs_dir/calls.txt'
|
|
|
16 --confidences '$text_outputs_dir/confidences.txt'
|
|
|
17 #if str($output_gender_estimate_cond.output_gender_estimate) == "yes"
|
|
|
18 --sex '$text_outputs_dir/gender_estimate.txt'
|
|
|
19 #end if
|
|
|
20 #if str($append_version) == "no":
|
|
|
21 --no-version
|
|
|
22 #end if
|
|
|
23 --output '$output'
|
|
|
24 --output_type $output_type
|
|
|
25 --threads \${GALAXY_SLOTS:-4}
|
|
|
26 ]]></command>
|
|
|
27 <inputs>
|
|
|
28 <param name="annot" type="data" format="csv" label="Probeset annotation file" />
|
|
|
29 <param name="fasta_ref" type="select" format="fasta" label="Fasta reference sequence">
|
|
|
30 <options from_data_table="all_fasta">
|
|
|
31 <column name="name" index="1"/>
|
|
|
32 <column name="value" index="2"/>
|
|
|
33 <column name="path" index="2"/>
|
|
|
34 <filter type="sort_by" column="1"/>
|
|
|
35 <validator type="no_options" message="No Fasta genome references are available. Use the Fetch Genome DBKeys All Fasta Data Manager tool in Galaxy to install and populate the all_fasta data table."/>
|
|
|
36 </options>
|
|
|
37 </param>
|
|
|
38 <conditional name="output_gender_estimate_cond">
|
|
|
39 <param name="output_gender_estimate" type="select" force_select="true" label="Output apt-probeset-genotype gender estimate?">
|
|
|
40 <option value="no" selected="true">No</option>
|
|
|
41 <option value="yes">Yes</option>
|
|
|
42 </param>
|
|
|
43 <when value="no" />
|
|
|
44 <when value="yes"/>
|
|
|
45 </conditional>
|
|
|
46 <conditional name="append_version_cond">
|
|
|
47 <param name="append_version" type="select" force_select="true" label="Append version and command line to the header?">
|
|
|
48 <option value="no" selected="true">No</option>
|
|
|
49 <option value="yes">Yes</option>
|
|
|
50 </param>
|
|
|
51 <when value="no" />
|
|
|
52 <when value="yes"/>
|
|
|
53 </conditional>
|
|
|
54 </inputs>
|
|
|
55 <outputs>
|
|
|
56 <collection name="txt_outputs" type="list" label="${tool.name} (reports) on ${on_string}">
|
|
|
57 <discover_datasets pattern="__name__" directory="output" format="txt" />
|
|
|
58 </collection>
|
|
|
59 <data name="output" format="vcf" />
|
|
|
60 </outputs>
|
|
|
61 <tests>
|
|
|
62 <test>
|
|
|
63 </test>
|
|
|
64 </tests>
|
|
|
65 <help>
|
|
|
66 This tool converts Affymetrix genotype calls and intensity files to VCF format.
|
|
|
67
|
|
|
68 -----
|
|
|
69
|
|
|
70 **Required options**
|
|
|
71
|
|
|
72 **Other options**
|
|
|
73 </help>
|
|
|
74 <citations>
|
|
|
75 <citation type="bibtex">
|
|
|
76 @misc{None,
|
|
|
77 journal = {None},
|
|
|
78 author = {Genovese, Giulio},
|
|
|
79 title = {None},
|
|
|
80 year = {None},
|
|
|
81 url = {https://github.com/freeseek/gtc2vcf},}
|
|
|
82 </citation>
|
|
|
83 </citations>
|
|
|
84 </tool>
|
