Mercurial > repos > devteam > vcfbreakcreatemulti
diff vcfbreakcreatemulti.xml @ 1:3aa04b92957f draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfbreakcreatemulti commit 0b9b6512272b82637c2f1e831367e89aed77ae79
| author | devteam |
|---|---|
| date | Thu, 15 Sep 2016 16:04:07 -0400 |
| parents | f0dae4ac267e |
| children | 690b1d846263 |
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--- a/vcfbreakcreatemulti.xml Thu Mar 19 12:43:19 2015 -0400 +++ b/vcfbreakcreatemulti.xml Thu Sep 15 16:04:07 2016 -0400 @@ -1,53 +1,48 @@ -<tool id="vcfbreakcreatemulti" name="VCFbreakCreateMulti:" version="0.0.3"> - <description>Break multiple alleles into multiple records, or combine overallpoing alleles into a single record</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"></expand> - <expand macro="stdio" /> - <command> - - #if str($break_or_create) == "break": - vcfbreakmulti "${input1}" > "${out_file1}" - #elif str($break_or_create) == "create": - vcfcreatemulti "${input1}" > "${out_file1}" - #end if - -</command> - - <inputs> - <param format="vcf" name="input1" type="data" label="Select VCF dataset"/> - <param name="break_or_create" type="select" display="radio" label="Break or Create?"> - <option value="break">Break</option> - <option value="create">Create</option> - </param> - </inputs> - <outputs> - <data format="vcf" name="out_file1" /> - </outputs> - <tests> - <test> - <param name="break_or_create" value="break"/> - <param name="input1" value="vcflib.vcf"/> - <output name="out_file1" file="vcfbreakcreatemulti-test1.vcf"/> - </test> - <test> - <param name="break_or_create" value="create"/> - <param name="input1" value="vcfbreakcreatemulti-test2-input.vcf"/> - <output name="out_file1" file="vcfbreakcreatemulti-test2.vcf"/> - </test> - </tests> - <help> - -This tool breaks or creates multiallelic VCF records based on user selection (**Break** or **Create**, respectively): - - - **Break** = If multiple alleles are specified in a single record, break the record into multiple lines, preserving allele-specific INFO fields. - - **Create** = If overlapping alleles are represented across multiple records, merge them into a single record. - ----- - -This tools is based on vcfbreakmulti and vcfcreatemulti utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). - -</help> - <expand macro="citations" /> -</tool> +<tool id="vcfbreakcreatemulti" name="VCFbreakCreateMulti:" version="@WRAPPER_VERSION@.0"> + <description>Break multiple alleles into multiple records, or combine overallpoing alleles into a single record</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio" /> + <command> + #if str($break_or_create) == "break": + vcfbreakmulti "${input1}" > "${out_file1}" + #elif str($break_or_create) == "create": + vcfcreatemulti "${input1}" > "${out_file1}" + #end if + </command> + <inputs> + <param format="vcf" name="input1" type="data" label="Select VCF dataset"/> + <param name="break_or_create" type="select" display="radio" label="Break or Create?"> + <option value="break">Break</option> + <option value="create">Create</option> + </param> + </inputs> + <outputs> + <data format="vcf" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="break_or_create" value="break"/> + <param name="input1" value="vcflib.vcf"/> + <output name="out_file1" file="vcfbreakcreatemulti-test1.vcf"/> + </test> + <test> + <param name="break_or_create" value="create"/> + <param name="input1" value="vcfbreakcreatemulti-test2-input.vcf"/> + <output name="out_file1" file="vcfbreakcreatemulti-test2.vcf"/> + </test> + </tests> + <help> +This tool breaks or creates multiallelic VCF records based on user selection (**Break** or **Create**, respectively): + + - **Break** = If multiple alleles are specified in a single record, break the record into multiple lines, preserving allele-specific INFO fields. + - **Create** = If overlapping alleles are represented across multiple records, merge them into a single record. + +---- + +This tools is based on vcfbreakmulti and vcfcreatemulti utilities from the VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). + </help> + <expand macro="citations" /> +</tool>