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comparison affy2vcf.xml @ 12:c5fc0983b98c draft

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author greg
date Fri, 12 Oct 2018 08:39:13 -0400
parents 55f227ba9972
children ea728b639a77
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11:55f227ba9972 12:c5fc0983b98c
12 --fasta-ref '$reference_genome_source_cond.history_item' 12 --fasta-ref '$reference_genome_source_cond.history_item'
13 #else: 13 #else:
14 --fasta-ref '$reference_genome_source_cond.locally_cached_item' 14 --fasta-ref '$reference_genome_source_cond.locally_cached_item'
15 #end if 15 #end if
16 --annot '$annot' 16 --annot '$annot'
17 --snp-posteriors '$text_outputs_dir/snp_posteriors.txt' 17 --snp-posteriors '$snp_posteriors'
18 --summary '$text_outputs_dir/summary.txt' 18 --summary '$summary'
19 --report '$text_outputs_dir/report.txt' 19 --report '$report'
20 --calls '$text_outputs_dir/calls.txt' 20 --calls '$calls'
21 --confidences '$text_outputs_dir/confidences.txt' 21 --confidences '$confidences'
22 #if str($output_gender_estimate) == "yes" 22 #if str($output_gender_estimate_cond.output_gender_estimate) == "yes"
23 --sex '$text_outputs_dir/gender_estimate.txt' 23 --sex '$gender_estimate'
24 #end if 24 #end if
25 #if str($append_version) == "no": 25 #if str($append_version) == "no":
26 --no-version 26 --no-version
27 #end if 27 #end if
28 --output '$output' 28 --output '$output'
29 --output-type $output_type 29 --output-type $output_type
30 --threads \${GALAXY_SLOTS:-4} 30 --threads \${GALAXY_SLOTS:-4}
31 ]]></command> 31 ]]></command>
32 <inputs> 32 <inputs>
33 <param name="annot" type="data" format="csv" label="Probeset annotation file" />
34 <conditional name="reference_genome_source_cond"> 33 <conditional name="reference_genome_source_cond">
35 <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?"> 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?">
36 <option value="history" selected="true">Use a reference genome from my history</option> 35 <option value="history" selected="true">Use a reference genome from my history</option>
37 <option value="cached">Use a locally cached genome index</option> 36 <option value="cached">Use a locally cached genome index</option>
38 </param> 37 </param>
49 <validator type="no_options" message="No cached Fasta genome references are available." /> 48 <validator type="no_options" message="No cached Fasta genome references are available." />
50 </options> 49 </options>
51 </param> 50 </param>
52 </when> 51 </when>
53 </conditional> 52 </conditional>
54 <param name="output_gender_estimate" type="select" force_select="true" label="Output apt-probeset-genotype gender estimate?"> 53 <param name="annot" type="data" format="csv" label="Probeset annotation file" />
55 <option value="no" selected="true">No</option> 54 <param name="summary" type="data" format="txt" label="Apt-probeset genotype summary file" />
56 <option value="yes">Yes</option> 55 <param name="snp_posteriors" type="data" format="txt" label="Apt-probeset genotype snp-posteriors file" />
57 </param> 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>
58 <param name="append_version" type="select" force_select="true" label="Append version and command line to the header?"> 67 <param name="append_version" type="select" force_select="true" label="Append version and command line to the header?">
59 <option value="no" selected="true">No</option> 68 <option value="no" selected="true">No</option>
60 <option value="yes">Yes</option> 69 <option value="yes">Yes</option>
61 </param> 70 </param>
62 <param name="output_type" type="select" force_select="true" label="Select format for output?"> 71 <param name="output_type" type="select" force_select="true" label="Select format for output?">
65 <option value="u" selected="true">Uncompressed BCF</option> 74 <option value="u" selected="true">Uncompressed BCF</option>
66 <option value="b">Compressed BCF</option> 75 <option value="b">Compressed BCF</option>
67 </param> 76 </param>
68 </inputs> 77 </inputs>
69 <outputs> 78 <outputs>
70 <collection name="txt_outputs" type="list" label="${tool.name} (reports) on ${on_string}">
71 <discover_datasets pattern="__name__" directory="output" format="txt" />
72 </collection>
73 <data name="output" format="vcf" /> 79 <data name="output" format="vcf" />
80 <data name="output_gender_estimate" format="txt" label="${tool.name} (gender estimate) on ${on_string}">
81 <filter>output_gender_estimate_cond['output_gender_estimate'] == "yes"</filter>
82 </data>
74 </outputs> 83 </outputs>
75 <tests> 84 <tests>
76 <test> 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"/>
77 </test> 95 </test>
78 </tests> 96 </tests>
79 <help> 97 <help>
80 This tool converts Affymetrix genotype calls and intensity files to VCF format. 98 This tool converts Affymetrix genotype calls and intensity files to VCF format.
81 99