Mercurial > repos > greg > affy2vcf

comparison affy2vcf.xml @ 5:8e6837a66351 draft

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author greg
date Fri, 05 Oct 2018 10:46:59 -0400
parents 5f30220af0cd
children 54dfcde738ad
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4:5f30220af0cd 5:8e6837a66351
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 #set text_outputs_dir = 'text_outputs' 7 #set text_outputs_dir = 'text_outputs'
8 mkdir $text_outputs_dir && 8 mkdir $text_outputs_dir &&
9 bcftools +affy2vcf.so 9 bcftools +affy2vcf.so
10 -- fasta_ref '$fasta_ref' 10 --fasta_ref '$reference_genome.fasta_ref'
11 --annot '$annot' 11 --annot '$annot'
12 --snp-posteriors '$text_outputs_dir/snp_posteriors.txt' 12 --snp-posteriors '$text_outputs_dir/snp_posteriors.txt'
13 --summary '$text_outputs_dir/summary.txt' 13 --summary '$text_outputs_dir/summary.txt'
14 --report '$text_outputs_dir/report.txt' 14 --report '$text_outputs_dir/report.txt'
15 --calls '$text_outputs_dir/calls.txt' 15 --calls '$text_outputs_dir/calls.txt'
24 --output_type $output_type 24 --output_type $output_type
25 --threads \${GALAXY_SLOTS:-4} 25 --threads \${GALAXY_SLOTS:-4}
26 ]]></command> 26 ]]></command>
27 <inputs> 27 <inputs>
28 <param name="annot" type="data" format="csv" label="Probeset annotation file" /> 28 <param name="annot" type="data" format="csv" label="Probeset annotation file" />
29 <param name="fasta_ref" type="select" format="fasta" label="Fasta reference sequence"> 29 <conditional name="reference_genome">
30 <options from_data_table="all_fasta"> 30 <param name="source" type="select" label="Will you select a reference reference genome from your history or use a locally cached genome index?">
31 <column name="name" index="1"/> 31 <option value="history" selected="true">Use a reference genome from my history</option>
32 <column name="value" index="2"/> 32 <option value="cached">Use a locally cached genome index</option>
33 <column name="path" index="2"/> 33 </param>
34 <filter type="sort_by" column="1"/> 34 <when value="history">
35 <validator type="no_options" message="No Fasta genome references are available. Use the Fetch Genome DBKeys All Fasta Data Manager tool in Galaxy to install and populate the all_fasta data table."/> 35 <param name="fasta_ref" type="data" format="fasta" label="Select reference genome" />
36 </options> 36 </when>
37 </param> 37 <when value="cached">
38 <param name="fasta_ref" type="select" format="fasta" label="Fasta reference sequence">
39 <options from_data_table="all_fasta">
40 <column name="name" index="1"/>
41 <column name="value" index="2"/>
42 <column name="path" index="2"/>
43 <filter type="sort_by" column="1"/>
44 <validator type="no_options" message="No cached Fasta genome references are available." />
45 </options>
46 </param>
47 </when>
48 </conditional>
38 <conditional name="output_gender_estimate_cond"> 49 <conditional name="output_gender_estimate_cond">
39 <param name="output_gender_estimate" type="select" force_select="true" label="Output apt-probeset-genotype gender estimate?"> 50 <param name="output_gender_estimate" type="select" force_select="true" label="Output apt-probeset-genotype gender estimate?">
40 <option value="no" selected="true">No</option> 51 <option value="no" selected="true">No</option>
41 <option value="yes">Yes</option> 52 <option value="yes">Yes</option>
42 </param> 53 </param>