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comparison affy2vcf.xml @ 0:a1e53778a82b draft

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author greg
date Fri, 12 Oct 2018 09:46:32 -0400
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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 export BCFTOOLS_PLUGINS=\$(dirname `which bcftools`)/../libexec/bcftools &&
9 mkdir $text_outputs_dir &&
10 bcftools +\$BCFTOOLS_PLUGINS/affy2vcf.so
11 #if str($reference_genome_source_cond.reference_genome_source) == "history":
12 --fasta-ref '$reference_genome_source_cond.history_item'
13 #else:
14 --fasta-ref '$reference_genome_source_cond.locally_cached_item'
15 #end if
16 --annot '$annot'
17 --snp-posteriors '$snp_posteriors'
18 --summary '$summary'
19 --report '$report'
20 --calls '$calls'
21 --confidences '$confidences'
22 #if str($output_gender_estimate_cond.output_gender_estimate) == "yes"
23 --sex '$gender_estimate'
24 #end if
25 #if str($append_version) == "no":
26 --no-version
27 #end if
28 --output '$output'
29 --output-type $output_type
30 --threads \${GALAXY_SLOTS:-4}
31 ]]></command>
32 <inputs>
33 <conditional name="reference_genome_source_cond">
34 <param name="reference_genome_source" type="select" label="Will you select a reference reference genome from your history or use a locally cached genome index?">
35 <option value="history" selected="true">Use a reference genome from my history</option>
36 <option value="cached">Use a locally cached genome index</option>
37 </param>
38 <when value="history">
39 <param name="history_item" type="data" format="fasta" label="Select reference genome" />
40 </when>
41 <when value="cached">
42 <param name="locally_cached_item" type="select" format="fasta" label="Fasta reference sequence">
43 <options from_data_table="all_fasta">
44 <column name="name" index="1"/>
45 <column name="value" index="2"/>
46 <column name="path" index="2"/>
47 <filter type="sort_by" column="1"/>
48 <validator type="no_options" message="No cached Fasta genome references are available." />
49 </options>
50 </param>
51 </when>
52 </conditional>
53 <param name="annot" type="data" format="csv" label="Probeset annotation file" />
54 <param name="summary" type="data" format="txt" label="Apt-probeset genotype summary file" />
55 <param name="snp_posteriors" type="data" format="txt" label="Apt-probeset genotype snp-posteriors file" />
56 <param name="report" type="data" format="txt" label="Apt-probeset genotype report file" />
57 <param name="confidences" type="data" format="txt" label="Apt-probeset genotype confidences file" />
58 <param name="calls" type="data" format="txt" label="Apt-probeset genotype calls file" />
59 <conditional name="output_gender_estimate_cond">
60 <param name="output_gender_estimate" type="select" force_select="true" label="Output apt-probeset-genotype gender estimate?">
61 <option value="no" selected="true">No</option>
62 <option value="yes">Yes</option>
63 </param>
64 <when value="no"/>
65 <when value="yes"/>
66 </conditional>
67 <param name="append_version" type="select" force_select="true" label="Append version and command line to the header?">
68 <option value="no" selected="true">No</option>
69 <option value="yes">Yes</option>
70 </param>
71 <param name="output_type" type="select" force_select="true" label="Select format for output?">
72 <option value="v" selected="true">Uncompressed VCF</option>
73 <option value="z">Compressed VCF</option>
74 <option value="u" selected="true">Uncompressed BCF</option>
75 <option value="b">Compressed BCF</option>
76 </param>
77 </inputs>
78 <outputs>
79 <data name="output" format="vcf" />
80 <data name="output_gender_estimate" format="txt" label="${tool.name} (gender estimate) on ${on_string}">
81 <filter>output_gender_estimate_cond['output_gender_estimate'] == "yes"</filter>
82 </data>
83 </outputs>
84 <tests>
85 <test>
86 <param name="reference_genome_source" value="history"/>
87 <param name="history_item" value="GCF_000222465.1_Adig_1.1_genomic.fna" ftype="fasta"/>
88 <param name="annot" value="annot.csv" ftype="csv"/>
89 <param name="summary" value="summary.txt" ftype="txt"/>
90 <param name="snp_posteriors" value="snp_posteriors.txt" ftype="txt"/>
91 <param name="report" value="report.txt" ftype="txt"/>
92 <param name="confidences" value="confidences.txt" ftype="txt"/>
93 <param name="calls" value="calls.txt" ftype="txt"/>
94 <output name="output" value="output.vcf" ftype="vcf"/>
95 </test>
96 </tests>
97 <help>
98 This tool converts Affymetrix genotype calls and intensity files to VCF format.
99
100 -----
101
102 **Required options**
103
104 **Other options**
105 </help>
106 <citations>
107 <citation type="bibtex">
108 @misc{None,
109 journal = {None},
110 author = {Genovese, Giulio},
111 title = {None},
112 year = {None},
113 url = {https://github.com/freeseek/gtc2vcf},}
114 </citation>
115 </citations>
116 </tool>