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comparison affy2vcf.xml @ 7:4dc497887a5c draft

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author greg
date Fri, 05 Oct 2018 11:09:55 -0400
parents 54dfcde738ad
children 192da25388ec
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6:54dfcde738ad 7:4dc497887a5c
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 $text_outputs_dir &&
9 bcftools +affy2vcf.so 9 bcftools +affy2vcf.so
10 --fasta_ref '$reference_genome.fasta_ref' 10 #if str($reference_genome_source_cond.reference_genome_source) == "history":
11 --fasta_ref '$reference_genome_source_cond.history_item'
12 #else:
13 --fasta_ref '$reference_genome_source_cond.locally_cached_item'
14 #end if
11 --annot '$annot' 15 --annot '$annot'
12 --snp-posteriors '$text_outputs_dir/snp_posteriors.txt' 16 --snp-posteriors '$text_outputs_dir/snp_posteriors.txt'
13 --summary '$text_outputs_dir/summary.txt' 17 --summary '$text_outputs_dir/summary.txt'
14 --report '$text_outputs_dir/report.txt' 18 --report '$text_outputs_dir/report.txt'
15 --calls '$text_outputs_dir/calls.txt' 19 --calls '$text_outputs_dir/calls.txt'
16 --confidences '$text_outputs_dir/confidences.txt' 20 --confidences '$text_outputs_dir/confidences.txt'
17 #if str($output_gender_estimate_cond.output_gender_estimate) == "yes" 21 #if str($output_gender_estimate) == "yes"
18 --sex '$text_outputs_dir/gender_estimate.txt' 22 --sex '$text_outputs_dir/gender_estimate.txt'
19 #end if 23 #end if
20 #if str($append_version_cond.append_version) == "no": 24 #if str($append_version) == "no":
21 --no-version 25 --no-version
22 #end if 26 #end if
23 --output '$output' 27 --output '$output'
24 --output_type $output_type 28 --output_type $output_type
25 --threads \${GALAXY_SLOTS:-4} 29 --threads \${GALAXY_SLOTS:-4}
26 ]]></command> 30 ]]></command>
27 <inputs> 31 <inputs>
28 <param name="annot" type="data" format="csv" label="Probeset annotation file" /> 32 <param name="annot" type="data" format="csv" label="Probeset annotation file" />
29 <conditional name="reference_genome"> 33 <conditional name="reference_genome_source_cond">
30 <param name="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?">
31 <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>
32 <option value="cached">Use a locally cached genome index</option> 36 <option value="cached">Use a locally cached genome index</option>
33 </param> 37 </param>
34 <when value="history"> 38 <when value="history">
35 <param name="fasta_ref" type="data" format="fasta" label="Select reference genome" /> 39 <param name="history_item" type="data" format="fasta" label="Select reference genome" />
36 </when> 40 </when>
37 <when value="cached"> 41 <when value="cached">
38 <param name="fasta_ref" type="select" format="fasta" label="Fasta reference sequence"> 42 <param name="locally_cached_item" type="select" format="fasta" label="Fasta reference sequence">
39 <options from_data_table="all_fasta"> 43 <options from_data_table="all_fasta">
40 <column name="name" index="1"/> 44 <column name="name" index="1"/>
41 <column name="value" index="2"/> 45 <column name="value" index="2"/>
42 <column name="path" index="2"/> 46 <column name="path" index="2"/>
43 <filter type="sort_by" column="1"/> 47 <filter type="sort_by" column="1"/>
44 <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." />
45 </options> 49 </options>
46 </param> 50 </param>
47 </when> 51 </when>
48 </conditional> 52 </conditional>
49 <conditional name="output_gender_estimate_cond"> 53 <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?"> 54 <option value="no" selected="true">No</option>
51 <option value="no" selected="true">No</option> 55 <option value="yes">Yes</option>
52 <option value="yes">Yes</option> 56 </param>
53 </param> 57 <param name="append_version" type="select" force_select="true" label="Append version and command line to the header?">
54 <when value="no" /> 58 <option value="no" selected="true">No</option>
55 <when value="yes"/> 59 <option value="yes">Yes</option>
56 </conditional> 60 </param>
57 <conditional name="append_version_cond"> 61 <param name="output_type" type="select" force_select="true" label="Select format for output?">
58 <param name="append_version" type="select" force_select="true" label="Append version and command line to the header?"> 62 <option value="v" selected="true">Uncompressed VCF</option>
59 <option value="no" selected="true">No</option> 63 <option value="z">Compressed VCF</option>
60 <option value="yes">Yes</option> 64 <option value="u" selected="true">Uncompressed BCF</option>
61 </param> 65 <option value="b">Compressed BCF</option>
62 <when value="no" /> 66 </param>
63 <when value="yes"/>
64 </conditional>
65 </inputs> 67 </inputs>
66 <outputs> 68 <outputs>
67 <collection name="txt_outputs" type="list" label="${tool.name} (reports) on ${on_string}"> 69 <collection name="txt_outputs" type="list" label="${tool.name} (reports) on ${on_string}">
68 <discover_datasets pattern="__name__" directory="output" format="txt" /> 70 <discover_datasets pattern="__name__" directory="output" format="txt" />
69 </collection> 71 </collection>