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comparison affy2vcf.xml @ 1:a2f0931898be draft

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author greg
date Thu, 25 Oct 2018 09:14:03 -0400
parents a1e53778a82b
children 02025c366fca
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0:a1e53778a82b 1:a2f0931898be
18 --summary '$summary' 18 --summary '$summary'
19 --report '$report' 19 --report '$report'
20 --calls '$calls' 20 --calls '$calls'
21 --confidences '$confidences' 21 --confidences '$confidences'
22 #if str($output_gender_estimate_cond.output_gender_estimate) == "yes" 22 #if str($output_gender_estimate_cond.output_gender_estimate) == "yes"
23 --sex '$gender_estimate' 23 --sex '$output_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 <param name="summary" type="data" format="txt" label="Apt-probeset genotype summary file" />
35 <param name="snp_posteriors" type="data" format="txt" label="Apt-probeset genotype snp-posteriors file" />
36 <param name="report" type="data" format="txt" label="Apt-probeset genotype report file" />
37 <param name="confidences" type="data" format="txt" label="Apt-probeset genotype confidences file" />
38 <param name="calls" type="data" format="txt" label="Apt-probeset genotype calls file" />
33 <conditional name="reference_genome_source_cond"> 39 <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?"> 40 <param name="reference_genome_source" type="select" label="Choose the source for the reference genome">
35 <option value="history" selected="true">Use a reference genome from my history</option> 41 <option value="history" selected="true">Use a reference genome from my history</option>
36 <option value="cached">Use a locally cached genome index</option> 42 <option value="cached">Use a locally cached genome index</option>
37 </param> 43 </param>
38 <when value="history"> 44 <when value="history">
39 <param name="history_item" type="data" format="fasta" label="Select reference genome" /> 45 <param name="history_item" type="data" format="fasta" label="Select reference genome" />
43 <options from_data_table="all_fasta"> 49 <options from_data_table="all_fasta">
44 <column name="name" index="1"/> 50 <column name="name" index="1"/>
45 <column name="value" index="2"/> 51 <column name="value" index="2"/>
46 <column name="path" index="2"/> 52 <column name="path" index="2"/>
47 <filter type="sort_by" column="1"/> 53 <filter type="sort_by" column="1"/>
48 <validator type="no_options" message="No cached Fasta genome references are available." /> 54 <validator type="no_options" message="No cached Fasta genome references are available for the build associated with the selected probeset annotation file." />
49 </options> 55 </options>
50 </param> 56 </param>
51 </when> 57 </when>
52 </conditional> 58 </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"> 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?"> 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> 61 <option value="no" selected="true">No</option>
62 <option value="yes">Yes</option> 62 <option value="yes">Yes</option>
63 </param> 63 </param>
66 </conditional> 66 </conditional>
67 <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?">
68 <option value="no" selected="true">No</option> 68 <option value="no" selected="true">No</option>
69 <option value="yes">Yes</option> 69 <option value="yes">Yes</option>
70 </param> 70 </param>
71 <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">
72 <option value="v" selected="true">Uncompressed VCF</option> 72 <option value="v" selected="true">Uncompressed VCF</option>
73 <option value="z">Compressed VCF</option> 73 <option value="z">Compressed VCF</option>
74 <option value="u" selected="true">Uncompressed BCF</option> 74 <option value="u" selected="true">Uncompressed BCF</option>
75 <option value="b">Compressed BCF</option> 75 <option value="b">Compressed BCF</option>
76 </param> 76 </param>
82 </data> 82 </data>
83 </outputs> 83 </outputs>
84 <tests> 84 <tests>
85 <test> 85 <test>
86 <param name="reference_genome_source" value="history"/> 86 <param name="reference_genome_source" value="history"/>
87 <param name="history_item" value="GCF_000222465.1_Adig_1.1_genomic.fna" ftype="fasta"/> 87 <param name="history_item" value="sub50_adig_genome.fasta" ftype="fasta"/>
88 <param name="annot" value="annot.csv" ftype="csv"/> 88 <param name="annot" value="axiom_acropsnp_coral_annotation.r1.csv" ftype="csv"/>
89 <param name="summary" value="summary.txt" ftype="txt"/> 89 <param name="summary" value="sub50_axiomgt1.summary.txt" ftype="txt"/>
90 <param name="snp_posteriors" value="snp_posteriors.txt" ftype="txt"/> 90 <param name="snp_posteriors" value="sub50_axiomgt1.snp_posteriors.txt" ftype="txt"/>
91 <param name="report" value="report.txt" ftype="txt"/> 91 <param name="report" value="axiomgt1.report.txt" ftype="txt"/>
92 <param name="confidences" value="confidences.txt" ftype="txt"/> 92 <param name="confidences" value="sub50_axiomgt1.confidences.txt" ftype="txt"/>
93 <param name="calls" value="calls.txt" ftype="txt"/> 93 <param name="calls" value="sub50_axiomgt1.calls.txt" ftype="txt"/>
94 <output name="output" value="output.vcf" ftype="vcf"/> 94 <output name="output" value="output.vcf" ftype="vcf"/>
95 </test> 95 </test>
96 </tests> 96 </tests>
97 <help> 97 <help>
98 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.
99 99
100 ----- 100 -----
101 101
102 **Required options** 102 **Required options**
103 103
104 * **Probeset annotation file** - probeset annotation file produced by the sequencing run.
105 * **Apt-probeset genotype summary file** - apt-probeset genotype summary file produced by the sequencing run.
106 * **Apt-probeset genotype snp-posteriors file** - apt-probeset genotype snp-posteriors file produced by the sequencing run.
107 * **Apt-probeset genotype report file** - apt-probeset genotype report file produced by the sequencing run.
108 * **Apt-probeset genotype confidences file** - apt-probeset genotype confidences file produced by the sequencing run.
109 * **Apt-probeset genotype calls file** - apt-probeset genotype calls file produced by the sequencing run.
110 * **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.
111
104 **Other options** 112 **Other options**
113
114 * **Output apt-probeset-genotype gender estimate** - output apt-probeset-genotype gender estimate into an additional dataset.
115 * **Append version and command line to the header** - append version and command line to the header of the output VCF dataset.
116 * **Select format for output** - select one of uncompressed/compressed VCF/BCF.
105 </help> 117 </help>
106 <citations> 118 <citations>
107 <citation type="bibtex"> 119 <citation type="bibtex">
108 @misc{None, 120 @misc{None,
109 journal = {None}, 121 journal = {None},