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comparison affy2vcf.xml @ 1:b8549f504829 draft

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author greg
date Thu, 16 May 2019 12:42:19 -0400
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0:5e9d8a4f6ac8 1:b8549f504829
1 <tool id="affy2vcf" name="Convert Affymetrix" version="@WRAPPER_VERSION@">
2 <description>genotype calls and intensities to VCF</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="1.9">bcftools-gtc2vcf-plugin</requirement>
8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[
10 @PREPARE_ENV@
11 #set text_outputs_dir = 'text_outputs'
12 mkdir $text_outputs_dir &&
13 bcftools +\$BCFTOOLS_PLUGINS/affy2vcf.so
14 #if str($reference_genome_source_cond.reference_genome_source) == "history":
15 --fasta-ref '$reference_genome_source_cond.history_item'
16 #else:
17 --fasta-ref '$reference_genome_source_cond.locally_cached_item.fields.path'
18 #end if
19 --annot '$annot'
20 --snp-posteriors '$snp_posteriors'
21 --summary '$summary'
22 --report '$report'
23 --calls '$calls'
24 --confidences '$confidences'
25 #if str($output_gender_estimate_cond.output_gender_estimate) == "yes"
26 --sex '$output_gender_estimate'
27 #end if
28 #if str($append_version) == "no":
29 --no-version
30 #end if
31 --output '$output'
32 --output-type $output_type
33 @THREADS@
34 ]]></command>
35 <inputs>
36 <param name="annot" type="data" format="csv" label="Probeset annotation file" />
37 <param name="summary" type="data" format="txt" label="Apt-probeset genotype summary file" />
38 <param name="snp_posteriors" type="data" format="txt" label="Apt-probeset genotype snp-posteriors file" />
39 <param name="report" type="data" format="txt" label="Apt-probeset genotype report file" />
40 <param name="confidences" type="data" format="txt" label="Apt-probeset genotype confidences file" />
41 <param name="calls" type="data" format="txt" label="Apt-probeset genotype calls file" />
42 <conditional name="reference_genome_source_cond">
43 <param name="reference_genome_source" type="select" label="Choose the source for the reference genome">
44 <option value="history" selected="true">Use a reference genome from my history</option>
45 <option value="cached">Use a locally cached genome index</option>
46 </param>
47 <when value="history">
48 <param name="history_item" type="data" format="fasta" label="Select reference genome" />
49 </when>
50 <when value="cached">
51 <param name="locally_cached_item" type="select" format="fasta" label="Fasta reference sequence">
52 <options from_data_table="all_fasta">
53 <column name="name" index="2"/>
54 <column name="value" index="0"/>
55 <column name="path" index="3"/>
56 <filter type="sort_by" column="1"/>
57 <validator type="no_options" message="No cached Fasta genome references are available for the build associated with the selected probeset annotation file." />
58 </options>
59 </param>
60 </when>
61 </conditional>
62 <conditional name="output_gender_estimate_cond">
63 <param name="output_gender_estimate" type="select" force_select="true" label="Output apt-probeset-genotype gender estimate?">
64 <option value="no" selected="true">No</option>
65 <option value="yes">Yes</option>
66 </param>
67 <when value="no"/>
68 <when value="yes"/>
69 </conditional>
70 <param name="append_version" type="select" force_select="true" label="Append version and command line to the header?">
71 <option value="no" selected="true">No</option>
72 <option value="yes">Yes</option>
73 </param>
74 <param name="output_type" type="select" force_select="true" label="Select format for output">
75 <option value="v" selected="true">Uncompressed VCF</option>
76 <option value="z">Compressed VCF</option>
77 <option value="u" selected="true">Uncompressed BCF</option>
78 <option value="b">Compressed BCF</option>
79 </param>
80 </inputs>
81 <outputs>
82 <expand macro="vcf_output"/>
83 <data name="output_gender_estimate" format="txt" label="${tool.name} (gender estimate) on ${on_string}">
84 <filter>output_gender_estimate_cond['output_gender_estimate'] == "yes"</filter>
85 </data>
86 </outputs>
87 <tests>
88 <test>
89 <param name="reference_genome_source" value="history"/>
90 <param name="history_item" value="GCF_000222465.1_Adig_1.1_genomic.fna" ftype="fasta"/>
91 <param name="annot" value="Axion_Acropsnp_coral_Annotation_r1.csv" ftype="csv"/>
92 <param name="summary" value="AxiomGT1.summary.txt" ftype="txt"/>
93 <param name="snp_posteriors" value="AxiomGT1.snp-posteriors.txt" ftype="txt"/>
94 <param name="report" value="AxiomGT1.report.txt" ftype="txt"/>
95 <param name="confidences" value="AxiomGT1.confidences.txt" ftype="txt"/>
96 <param name="calls" value="AxiomGT1.calls.txt" ftype="txt"/>
97 <output name="output" value="output.vcf" ftype="vcf"/>
98 </test>
99 </tests>
100 <help>
101 This tool converts Affymetrix genotype calls and intensity files to VCF format.
102
103 -----
104
105 **Required options**
106
107 * **Probeset annotation file** - probeset annotation file produced by the sequencing run.
108 * **Apt-probeset genotype summary file** - apt-probeset genotype summary file produced by the sequencing run.
109 * **Apt-probeset genotype snp-posteriors file** - apt-probeset genotype snp-posteriors file produced by the sequencing run.
110 * **Apt-probeset genotype report file** - apt-probeset genotype report file produced by the sequencing run.
111 * **Apt-probeset genotype confidences file** - apt-probeset genotype confidences file produced by the sequencing run.
112 * **Apt-probeset genotype calls file** - apt-probeset genotype calls file produced by the sequencing run.
113 * **Choose the source for the reference genome** - select a reference genome from your history or one installed into your local Galaxy environment by a data manager tool.
114
115 **Other options**
116
117 * **Output apt-probeset-genotype gender estimate** - output apt-probeset-genotype gender estimate into an additional dataset.
118 * **Append version and command line to the header** - append version and command line to the header of the output VCF dataset.
119 * **Select format for output** - select one of uncompressed/compressed VCF/BCF.
120 </help>
121 <citations>
122 <expand macro="citation1"/>
123 <citation type="bibtex">
124 @misc{None,
125 journal = {None},
126 author = {Genovese, Giulio},
127 title = {None},
128 year = {None},
129 url = {https://github.com/freeseek/gtc2vcf},}
130 </citation>
131 </citations>
132 </tool>