Mercurial > repos > devteam > vcfcheck

annotate vcfcheck.xml @ 0:3ee22bc13811 draft

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