Mercurial > repos > devteam > vcfsort
changeset 1:586f4536fc65 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfsort commit b94a1012a2c76e77564f504543e90a692a8de562
| author | devteam |
|---|---|
| date | Mon, 03 Oct 2016 11:22:55 -0400 |
| parents | 59d4413e75eb |
| children | d92d6f631ff5 |
| files | macros.xml vcfsort.xml |
| diffstat | 2 files changed, 32 insertions(+), 28 deletions(-) [+] |
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--- a/macros.xml Mon Nov 09 12:34:33 2015 -0500 +++ b/macros.xml Mon Oct 03 11:22:55 2016 -0400 @@ -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">
--- a/vcfsort.xml Mon Nov 09 12:34:33 2015 -0500 +++ b/vcfsort.xml Mon Oct 03 11:22:55 2016 -0400 @@ -1,27 +1,30 @@ -<tool id="vcfsort" name="VCFsort:" version="0.0.2"> - <description>Sort VCF dataset by coordinate</description> - <command>(grep ^"#" "${input1}"; grep -v ^"#" "${input1}" | LC_ALL=C sort -k1,1 -k2,2n -V) > "${out_file1}"</command> - <inputs> - <param format="vcf" name="input1" type="data" label="Select VCF dataset"/> - </inputs> - <outputs> - <data format="vcf" name="out_file1" /> - </outputs> - <tests> - <test> - <param name="input1" value="vcfsort-test1-input.vcf"/> - <output name="out_file1" file="vcfsort-test1.vcf"/> - </test> - </tests> - <help> - -This tool uses native UNIX sort command to order VCF dataset in coordinate order. For technically inclined the command is:: - - (grep ^"#" INPUT_file ; grep -v ^"#" INPUT_file | LC_ALL=C sort -k1,1 -k2,2n -V) > OUTPUT_file - -.. class:: infomark - -The same result can be achieved with the Galaxy's general purpose sort tool (in this case sort on the first and the second column in ascending order). - -</help> -</tool> +<tool id="vcfsort" name="VCFsort:" version="@WRAPPER_VERSION@.0"> + <description>Sort VCF dataset by coordinate</description> + <macros> + <import>macros.xml</import> + </macros> + <command>(grep ^"#" "${input1}"; grep -v ^"#" "${input1}" | LC_ALL=C sort -k1,1 -k2,2n -V) > "${out_file1}"</command> + <inputs> + <param format="vcf" name="input1" type="data" label="Select VCF dataset"/> + </inputs> + <outputs> + <data format="vcf" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="input1" value="vcfsort-test1-input.vcf"/> + <output name="out_file1" file="vcfsort-test1.vcf"/> + </test> + </tests> + <help> + +This tool uses native UNIX sort command to order VCF dataset in coordinate order. For technically inclined the command is:: + + (grep ^"#" INPUT_file ; grep -v ^"#" INPUT_file | LC_ALL=C sort -k1,1 -k2,2n -V) > OUTPUT_file + +.. class:: infomark + +The same result can be achieved with the Galaxy's general purpose sort tool (in this case sort on the first and the second column in ascending order). + +</help> +</tool>