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view vcfcheck.xml @ 1:ef00ee1f1842 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcheck commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
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date | Thu, 12 Nov 2015 09:59:10 -0500 |
parents | 3ee22bc13811 |
children | 265e5230925c |
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<tool id="vcfcheck" name="VCFcheck:" version="0.0.3"> <description>Verify that the reference allele matches the reference genome</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"></expand> <command> #set $reference_fasta_filename = "localref.fa" #if str( $reference_source.reference_source_selector ) == "history": ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && #else: #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) #end if vcfcheck $failure_selector -f "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"</command> <inputs> <conditional name="reference_source"> <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> <option value="cached">Locally cached</option> <option value="history">History</option> </param> <when value="cached"> <param name="ref_file" type="select" label="Select reference genome"> <options from_data_table="fasta_indexes"> <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>--> </options> <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> </param> <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset"> <!-- Validators are commented to allow users apply too to any build. May need to be revised in the future <validator type="unspecified_build" /> <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." /> --> </param> </when> <when value="history"> <!-- FIX ME!!!! --> <param name="ref_file" type="data" format="fasta" label="Using reference file" /> <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset" /> </when> </conditional> <param name="failure_selector" type="select" display="radio" label="Exclude or include failed sites"> <option value="-x">Exculde failures (-x option)</option> <option value="-k">Keep failures (-k option)</option> </param> </inputs> <outputs> <data format="vcf" name="out_file1" /> </outputs> <stdio> <regex match="index file" source="stderr" level="warning"/> </stdio> <tests> <test> <param name="reference_source_selector" value="history" /> <param name="failure_selection" value="-x" /> <param name="input_vcf" value="vcflib-phix.vcf"/> <param name="ref_file" value="vcflib-test-genome-phix.fa" /> <output name="out_file1" file="vcfcheck-test1.vcf"/> </test> </tests> <help> Verifies that the VCF REF field matches the reference as described. The options are:: -x, --exclude-failures If a record fails, don't print it. Otherwise do. -k, --keep-failures Print if the record fails, otherwise not. ---- Vcfcheck @IS_PART_OF_VCFLIB@ </help> <expand macro="citations" /> </tool>