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comparison vcfcheck.xml @ 0:42e3f0702878

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Imported from capsule None
author anton
date Wed, 11 Jun 2014 17:11:46 -0400
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children 27478240ba22
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1 <tool id="vcfcheck" name="VCFcheck:" version="0.0.1">
2 <requirements>
3 <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement>
4 </requirements>
5 <description>Verify that the reference allele matches the reference genome</description>
6 <command>
7 #set $reference_fasta_filename = "localref.fa"
8 #if str( $reference_source.reference_source_selector ) == "history":
9 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
10 #else:
11 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
12 #end if
13 vcfcheck $failure_selector -f "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"</command>
14 <inputs>
15 <conditional name="reference_source">
16 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
17 <option value="cached">Locally cached</option>
18 <option value="history">History</option>
19 </param>
20 <when value="cached">
21 <param name="ref_file" type="select" label="Select reference genome">
22 <options from_data_table="fasta_indexes">
23 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
24 </options>
25 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
26 </param>
27 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset">
28 <!-- Validators are commented to allow users apply too to any build. May need to be revised in the future
29 <validator type="unspecified_build" />
30 <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
31 -->
32 </param>
33 </when>
34 <when value="history"> <!-- FIX ME!!!! -->
35 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
36 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset" />
37 </when>
38 </conditional>
39 <param name="failure_selector" type="select" display="radio" label="Exclude or include failed sites">
40 <option value="-x">Exculde failures (-x option)</option>
41 <option value="-k">Keep failures (-k option)</option>
42 </param>
43 </inputs>
44 <outputs>
45 <data format="vcf" name="out_file1" />
46 </outputs>
47 <stdio>
48 <regex match="index file" source="stderr" level="warning"/>
49 </stdio>
50 <tests>
51 <test>
52 <param name="reference_source_selector" value="history" />
53 <param name="failure_selection" value="-x" />
54 <param name="input_vcf" value="vcflib-phix.vcf"/>
55 <param name="ref_file" value="vcflib-test-genome-phix.fa" />
56 <output name="out_file1" file="vcfcheck-test1.vcf"/>
57 </test>
58 </tests>
59 <help>
60
61 Verifies that the VCF REF field matches the reference as described.
62
63 The options are::
64
65 -x, --exclude-failures If a record fails, don't print it. Otherwise do.
66 -k, --keep-failures Print if the record fails, otherwise not.
67
68 ----
69
70 Vcfcheck is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
71
72 </help>
73 </tool>