comparison vcfcheck.xml @ 0:3ee22bc13811 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcheck commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:30:30 -0500
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children 265e5230925c
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-1:000000000000 0:3ee22bc13811
1 <tool id="vcfcheck" name="VCFcheck:" version="0.0.3">
2 <description>Verify that the reference allele matches the reference genome</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"></expand>
7 <command>
8 #set $reference_fasta_filename = "localref.fa"
9 #if str( $reference_source.reference_source_selector ) == "history":
10 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
11 #else:
12 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
13 #end if
14 vcfcheck $failure_selector -f "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"</command>
15 <inputs>
16 <conditional name="reference_source">
17 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
18 <option value="cached">Locally cached</option>
19 <option value="history">History</option>
20 </param>
21 <when value="cached">
22 <param name="ref_file" type="select" label="Select reference genome">
23 <options from_data_table="fasta_indexes">
24 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
25 </options>
26 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
27 </param>
28 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset">
29 <!-- Validators are commented to allow users apply too to any build. May need to be revised in the future
30 <validator type="unspecified_build" />
31 <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." />
32 -->
33 </param>
34 </when>
35 <when value="history"> <!-- FIX ME!!!! -->
36 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
37 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset" />
38 </when>
39 </conditional>
40 <param name="failure_selector" type="select" display="radio" label="Exclude or include failed sites">
41 <option value="-x">Exculde failures (-x option)</option>
42 <option value="-k">Keep failures (-k option)</option>
43 </param>
44 </inputs>
45 <outputs>
46 <data format="vcf" name="out_file1" />
47 </outputs>
48 <stdio>
49 <regex match="index file" source="stderr" level="warning"/>
50 </stdio>
51 <tests>
52 <test>
53 <param name="reference_source_selector" value="history" />
54 <param name="failure_selection" value="-x" />
55 <param name="input_vcf" value="vcflib-phix.vcf"/>
56 <param name="ref_file" value="vcflib-test-genome-phix.fa" />
57 <output name="out_file1" file="vcfcheck-test1.vcf"/>
58 </test>
59 </tests>
60 <help>
61
62 Verifies that the VCF REF field matches the reference as described.
63
64 The options are::
65
66 -x, --exclude-failures If a record fails, don't print it. Otherwise do.
67 -k, --keep-failures Print if the record fails, otherwise not.
68
69 ----
70
71 Vcfcheck @IS_PART_OF_VCFLIB@
72 </help>
73 <expand macro="citations" />
74 </tool>