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comparison affy2vcf.xml @ 14:640d50a57063 draft

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author greg
date Thu, 01 Nov 2018 09:09:53 -0400
parents ea728b639a77
children 5b64c88d706f
comparison
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13:ea728b639a77 14:640d50a57063
1 <tool id="affr2vcf" name="Convert Affymetrix" version="1.9"> 1 <tool id="affr2vcf" name="Convert Affymetrix" version="@WRAPPER_VERSION@">
2 <description>genotype calls and intensities to VCF</description> 2 <description>genotype calls and intensities to VCF</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="1.9">bcftools-gtc2vcf-plugin</requirement> 7 <requirement type="package" version="1.9">bcftools-gtc2vcf-plugin</requirement>
5 </requirements> 8 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 @PREPARE_ENV@
7 #set text_outputs_dir = 'text_outputs' 11 #set text_outputs_dir = 'text_outputs'
8 export BCFTOOLS_PLUGINS=\$(dirname `which bcftools`)/../libexec/bcftools &&
9 mkdir $text_outputs_dir && 12 mkdir $text_outputs_dir &&
10 bcftools +\$BCFTOOLS_PLUGINS/affy2vcf.so 13 bcftools +\$BCFTOOLS_PLUGINS/affy2vcf.so
11 #if str($reference_genome_source_cond.reference_genome_source) == "history": 14 #if str($reference_genome_source_cond.reference_genome_source) == "history":
12 --fasta-ref '$reference_genome_source_cond.history_item' 15 --fasta-ref '$reference_genome_source_cond.history_item'
13 #else: 16 #else:
25 #if str($append_version) == "no": 28 #if str($append_version) == "no":
26 --no-version 29 --no-version
27 #end if 30 #end if
28 --output '$output' 31 --output '$output'
29 --output-type $output_type 32 --output-type $output_type
30 --threads \${GALAXY_SLOTS:-4} 33 @THREADS@
31 ]]></command> 34 ]]></command>
32 <inputs> 35 <inputs>
33 <param name="annot" type="data" format="csv" label="Probeset annotation file" /> 36 <param name="annot" type="data" format="csv" label="Probeset annotation file" />
34 <param name="summary" type="data" format="txt" label="Apt-probeset genotype summary file" /> 37 <param name="summary" type="data" format="txt" label="Apt-probeset genotype summary file" />
35 <param name="snp_posteriors" type="data" format="txt" label="Apt-probeset genotype snp-posteriors file" /> 38 <param name="snp_posteriors" type="data" format="txt" label="Apt-probeset genotype snp-posteriors file" />
74 <option value="u" selected="true">Uncompressed BCF</option> 77 <option value="u" selected="true">Uncompressed BCF</option>
75 <option value="b">Compressed BCF</option> 78 <option value="b">Compressed BCF</option>
76 </param> 79 </param>
77 </inputs> 80 </inputs>
78 <outputs> 81 <outputs>
79 <data name="output" format="vcf" /> 82 <expand macro="vcf_output"/>
80 <data name="output_gender_estimate" format="txt" label="${tool.name} (gender estimate) on ${on_string}"> 83 <data name="output_gender_estimate" format="txt" label="${tool.name} (gender estimate) on ${on_string}">
81 <filter>output_gender_estimate_cond['output_gender_estimate'] == "yes"</filter> 84 <filter>output_gender_estimate_cond['output_gender_estimate'] == "yes"</filter>
82 </data> 85 </data>
83 </outputs> 86 </outputs>
84 <tests> 87 <tests>
114 * **Output apt-probeset-genotype gender estimate** - output apt-probeset-genotype gender estimate into an additional dataset. 117 * **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. 118 * **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. 119 * **Select format for output** - select one of uncompressed/compressed VCF/BCF.
117 </help> 120 </help>
118 <citations> 121 <citations>
122 <expand macro="citation1"/>
119 <citation type="bibtex"> 123 <citation type="bibtex">
120 @misc{None, 124 @misc{None,
121 journal = {None}, 125 journal = {None},
122 author = {Genovese, Giulio}, 126 author = {Genovese, Giulio},
123 title = {None}, 127 title = {None},