| Previous changeset 1:046b3db333bd (2015-11-11) Next changeset 3:5e850c85ba32 (2018-03-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfcheck commit 0b9b6512272b82637c2f1e831367e89aed77ae79 |
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modified:
macros.xml vcfcheck.xml |
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removed:
tool_dependencies.xml |
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| diff -r 046b3db333bd -r 40a339e4692e macros.xml --- a/macros.xml Wed Nov 11 12:58:33 2015 -0500 +++ b/macros.xml Thu Sep 15 16:04:23 2016 -0400 |
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| @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="8a5602bf07">vcflib</requirement> + <requirement type="package" version="1.0.0_rc1">vcflib</requirement> <yield/> </requirements> </xml> @@ -10,6 +10,7 @@ <exit_code range="1:" level="fatal" /> </stdio> </xml> + <token name="@WRAPPER_VERSION@">1.0.0_rc1</token> <xml name="citations"> <citations> <citation type="bibtex"> |
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| diff -r 046b3db333bd -r 40a339e4692e tool_dependencies.xml --- a/tool_dependencies.xml Wed Nov 11 12:58:33 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="vcflib" version="8a5602bf07"> - <repository changeset_revision="7e67466b033e" name="package_vcflib_8a5602bf07" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |
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| diff -r 046b3db333bd -r 40a339e4692e vcfcheck.xml --- a/vcfcheck.xml Wed Nov 11 12:58:33 2015 -0500 +++ b/vcfcheck.xml Thu Sep 15 16:04:23 2016 -0400 |
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| @@ -1,74 +1,74 @@ -<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> +<tool id="vcfcheck" name="VCFcheck:" version="@WRAPPER_VERSION@.0"> + <description>Verify that the reference allele matches the reference genome</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"></expand> + <stdio> + <regex match="index file" source="stderr" level="warning"/> + </stdio> + <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> + <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> |