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comparison affy2vcf.xml @ 4:5f30220af0cd draft

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author greg
date Thu, 04 Oct 2018 10:34:37 -0400
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3:4bf7233a372b 4:5f30220af0cd
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>