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comparison vcfcheck.xml @ 2:265e5230925c draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcheck commit 0b9b6512272b82637c2f1e831367e89aed77ae79
author devteam
date Thu, 15 Sep 2016 16:03:14 -0400
parents 3ee22bc13811
children 713575be4f77
comparison
equal deleted inserted replaced
1:ef00ee1f1842 2:265e5230925c
1 <tool id="vcfcheck" name="VCFcheck:" version="0.0.3"> 1 <tool id="vcfcheck" name="VCFcheck:" version="@WRAPPER_VERSION@.0">
2 <description>Verify that the reference allele matches the reference genome</description> 2 <description>Verify that the reference allele matches the reference genome</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"></expand> 6 <expand macro="requirements"></expand>
7 <command> 7 <stdio>
8 #set $reference_fasta_filename = "localref.fa" 8 <regex match="index file" source="stderr" level="warning"/>
9 #if str( $reference_source.reference_source_selector ) == "history": 9 </stdio>
10 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp; 10 <command>
11 #else: 11 #set $reference_fasta_filename = "localref.fa"
12 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) 12 #if str( $reference_source.reference_source_selector ) == "history":
13 #end if 13 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
14 vcfcheck $failure_selector -f "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"</command> 14 #else:
15 <inputs> 15 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
16 <conditional name="reference_source"> 16 #end if
17 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> 17 vcfcheck $failure_selector -f "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"</command>
18 <option value="cached">Locally cached</option> 18 <inputs>
19 <option value="history">History</option> 19 <conditional name="reference_source">
20 </param> 20 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
21 <when value="cached"> 21 <option value="cached">Locally cached</option>
22 <param name="ref_file" type="select" label="Select reference genome"> 22 <option value="history">History</option>
23 <options from_data_table="fasta_indexes"> 23 </param>
24 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>--> 24 <when value="cached">
25 </options> 25 <param name="ref_file" type="select" label="Select reference genome">
26 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 26 <options from_data_table="fasta_indexes">
27 </param> 27 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
28 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset"> 28 </options>
29 <!-- Validators are commented to allow users apply too to any build. May need to be revised in the future 29 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
30 <validator type="unspecified_build" /> 30 </param>
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." /> 31 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset">
32 --> 32 <!-- Validators are commented to allow users apply too to any build. May need to be revised in the future
33 </param> 33 <validator type="unspecified_build" />
34 </when> 34 <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." />
35 <when value="history"> <!-- FIX ME!!!! --> 35 -->
36 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> 36 </param>
37 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset" /> 37 </when>
38 </when> 38 <when value="history"> <!-- FIX ME!!!! -->
39 </conditional> 39 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
40 <param name="failure_selector" type="select" display="radio" label="Exclude or include failed sites"> 40 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset" />
41 <option value="-x">Exculde failures (-x option)</option> 41 </when>
42 <option value="-k">Keep failures (-k option)</option> 42 </conditional>
43 </param> 43 <param name="failure_selector" type="select" display="radio" label="Exclude or include failed sites">
44 </inputs> 44 <option value="-x">Exculde failures (-x option)</option>
45 <outputs> 45 <option value="-k">Keep failures (-k option)</option>
46 <data format="vcf" name="out_file1" /> 46 </param>
47 </outputs> 47 </inputs>
48 <stdio> 48 <outputs>
49 <regex match="index file" source="stderr" level="warning"/> 49 <data format="vcf" name="out_file1" />
50 </stdio> 50 </outputs>
51 <tests> 51 <tests>
52 <test> 52 <test>
53 <param name="reference_source_selector" value="history" /> 53 <param name="reference_source_selector" value="history" />
54 <param name="failure_selection" value="-x" /> 54 <param name="failure_selection" value="-x" />
55 <param name="input_vcf" value="vcflib-phix.vcf"/> 55 <param name="input_vcf" value="vcflib-phix.vcf"/>
56 <param name="ref_file" value="vcflib-test-genome-phix.fa" /> 56 <param name="ref_file" value="vcflib-test-genome-phix.fa" />
57 <output name="out_file1" file="vcfcheck-test1.vcf"/> 57 <output name="out_file1" file="vcfcheck-test1.vcf"/>
58 </test> 58 </test>
59 </tests> 59 </tests>
60 <help> 60 <help>
61 61
62 Verifies that the VCF REF field matches the reference as described. 62 Verifies that the VCF REF field matches the reference as described.
63 63
64 The options are:: 64 The options are::
65 65
67 -k, --keep-failures Print if the record fails, otherwise not. 67 -k, --keep-failures Print if the record fails, otherwise not.
68 68
69 ---- 69 ----
70 70
71 Vcfcheck @IS_PART_OF_VCFLIB@ 71 Vcfcheck @IS_PART_OF_VCFLIB@
72 </help> 72 </help>
73 <expand macro="citations" /> 73 <expand macro="citations" />
74 </tool> 74 </tool>