Mercurial > repos > devteam > vcf2tsv
diff vcf2tsv.xml @ 2:8fb92fcd20ae draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
| author | devteam |
|---|---|
| date | Thu, 15 Sep 2016 16:06:22 -0400 |
| parents | d6c944f1581a |
| children | e92b3c0f9224 |
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--- a/vcf2tsv.xml Thu Mar 19 12:19:17 2015 -0400 +++ b/vcf2tsv.xml Thu Sep 15 16:06:22 2016 -0400 @@ -1,46 +1,45 @@ -<tool id="vcf2tsv" name="VCFtoTab-delimited:" version="0.0.3"> - <description>Convert VCF data into TAB-delimited format</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"></expand> - <expand macro="stdio" /> - <command>vcf2tsv ${g_option} -n "${null_filler}" "${input}" > "${out_file1}"</command> - <inputs> - <param format="vcf" name="input" type="data" label="Select VCF dataset to convert"/> - <param name="g_option" type="boolean" checked="true" truevalue="-g" falsevalue="" label="Report data per sample" help="-g option"/> - <param name="null_filler" type="select" label="Fill empty fields with" help="-n option" > - <option value="">Nothing</option> - <option value=".">.</option> - <option value="*">*</option> - <option value="NULL">NULL</option> - </param> - </inputs> - <outputs> - <data format="tabular" name="out_file1" /> - </outputs> - <tests> - <test> - <param name="g_option" value="true"/> - <param name="null_filler" value="."/> - <param name="input" value="vcflib.vcf"/> - <output name="out_file1" file="vcf2tsv-test1.tab"/> - </test> - <test> - <param name="g_option" value="false"/> - <param name="null_filler" value="."/> - <param name="input" value="vcflib.vcf"/> - <output name="out_file1" file="vcf2tsv-test2.tab"/> - </test> - </tests> - <help> - -Converts VCF dataset to tab-delimited format, using null string to replace empty values in the table. -Specifying "**Report data per sample**" (-g) will output one line per sample with genotype information. - ----- - -Vcf2Tsv @IS_PART_OF_VCFLIB@ -</help> - <expand macro="citations" /> -</tool> +<tool id="vcf2tsv" name="VCFtoTab-delimited:" version="@WRAPPER_VERSION@.0"> + <description>Convert VCF data into TAB-delimited format</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio" /> + <command>vcf2tsv ${g_option} -n '${null_filler}' '${input}' > '${out_file1}'</command> + <inputs> + <param format="vcf" name="input" type="data" label="Select VCF dataset to convert"/> + <param name="g_option" type="boolean" checked="true" truevalue="-g" falsevalue="" label="Report data per sample" help="-g option"/> + <param name="null_filler" type="select" label="Fill empty fields with" help="-n option" > + <option value="">Nothing</option> + <option value=".">.</option> + <option value="*">*</option> + <option value="NULL">NULL</option> + </param> + </inputs> + <outputs> + <data format="tabular" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="g_option" value="true"/> + <param name="null_filler" value="."/> + <param name="input" value="vcflib.vcf"/> + <output name="out_file1" file="vcf2tsv-test1.tab"/> + </test> + <test> + <param name="g_option" value="false"/> + <param name="null_filler" value="."/> + <param name="input" value="vcflib.vcf"/> + <output name="out_file1" file="vcf2tsv-test2.tab"/> + </test> + </tests> + <help> +Converts VCF dataset to tab-delimited format, using null string to replace empty values in the table. +Specifying "**Report data per sample**" (-g) will output one line per sample with genotype information. + +---- + +Vcf2Tsv @IS_PART_OF_VCFLIB@ + </help> + <expand macro="citations" /> +</tool>