| Previous changeset 1:d6c944f1581a (2015-03-19) Next changeset 3:e92b3c0f9224 (2018-03-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79 |
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modified:
macros.xml test-data/vcf2tsv-test1.tab vcf2tsv.xml |
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removed:
tool_dependencies.xml |
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| diff -r d6c944f1581a -r 8fb92fcd20ae macros.xml --- a/macros.xml Thu Mar 19 12:19:17 2015 -0400 +++ b/macros.xml Thu Sep 15 16:06:22 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 d6c944f1581a -r 8fb92fcd20ae test-data/vcf2tsv-test1.tab --- a/test-data/vcf2tsv-test1.tab Thu Mar 19 12:19:17 2015 -0400 +++ b/test-data/vcf2tsv-test1.tab Thu Sep 15 16:06:22 2016 -0400 |
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| @@ -22,6 +22,7 @@ 20 1234567 microsat1 G GA,GAC 50 PASS G 3,1 . 6 9 3 0 0 NA00003 3 40 1/1 . 20 1235237 . T . 0 . . . . . . . 0 0 NA00001 . . 0/0 . 20 1235237 . T . 0 . . . . . . . 0 0 NA00002 . . 0|0 . +20 1235237 . T . 0 . . . . . . . 0 0 NA00003 . . ./. . X 10 rsTest AC A,ATG 10 PASS . . . . . . 0 0 NA00001 . . 0 . X 10 rsTest AC A,ATG 10 PASS . . . . . . 0 0 NA00002 . . 0/1 . X 10 rsTest AC A,ATG 10 PASS . . . . . . 0 0 NA00003 . . 0|2 . |
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| diff -r d6c944f1581a -r 8fb92fcd20ae tool_dependencies.xml --- a/tool_dependencies.xml Thu Mar 19 12:19:17 2015 -0400 +++ /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 d6c944f1581a -r 8fb92fcd20ae vcf2tsv.xml --- a/vcf2tsv.xml Thu Mar 19 12:19:17 2015 -0400 +++ b/vcf2tsv.xml Thu Sep 15 16:06:22 2016 -0400 |
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| @@ -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> |