Mercurial > repos > devteam > vcfrandomsample
changeset 1:03030ecd1961 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 0b9b6512272b82637c2f1e831367e89aed77ae79
| author | devteam |
|---|---|
| date | Thu, 15 Sep 2016 16:05:17 -0400 |
| parents | ad12ba1db0e4 |
| children | 939834d8de40 |
| files | macros.xml tool_dependencies.xml vcfrandomsample.xml |
| diffstat | 3 files changed, 57 insertions(+), 62 deletions(-) [+] |
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--- a/macros.xml Mon Nov 09 12:33:58 2015 -0500 +++ b/macros.xml Thu Sep 15 16:05:17 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/tool_dependencies.xml Mon Nov 09 12:33:58 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="vcflib" version="8a5602bf07"> - <repository changeset_revision="3ac0905f7b7c" name="package_vcflib_8a5602bf07" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>
--- a/vcfrandomsample.xml Mon Nov 09 12:33:58 2015 -0500 +++ b/vcfrandomsample.xml Thu Sep 15 16:05:17 2016 -0400 @@ -1,55 +1,55 @@ -<tool id="vcfrandomsample" name="VCFrandomSample:" version="0.0.3"> - <description>Randomly sample sites from VCF dataset</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"></expand> - <expand macro="stdio" /> - <command> - - #if $adv_options.adv_options_selector == True: - vcfrandomsample -s "${adv_options.scale_by}" -p ${random_seed} -r ${rate} "${vcf_input}" > "${out_file1}" - #else: - vcfrandomsample -p ${random_seed} -r ${rate} "${vcf_input}" > "${out_file1}" - #end if - </command> - <inputs> - <param format="vcf" name="vcf_input" type="data" label="Select random sites from"/> - <param name="rate" type="float" value="0.1" label="base sampling probability per locus" help="-r, --rate"/> - <param name="random_seed" type="integer" value="17823618326" label="use this random seed" help="-p, --random-seed; use this to make results reproducible" /> - <conditional name="adv_options"> - <param name="adv_options_selector" type="boolean" truevalue="use_adv_controls" label="Advanced controls" help="Allows you to specify options that are not listed above"/> - <when value="use_adv_controls"> - <param name="scale_by" type="text" value="AF" label="scale sampling likelihood by this INFO field" help="-s, --scale-by; this only works for Float info fields such as AF" /> - </when> - </conditional> - </inputs> - <outputs> - <data format="vcf" name="out_file1" /> - </outputs> - <tests> - <test> - <param name="vcf_input" value="vcflib.vcf"/> - <param name="rate" value="0.2" /> - <param name="random_seed" value="1" /> - <param name="adv_options_selector" value="False" /> - <output name="out_file1" file="vcfrandomsample-test1.vcf" lines_diff="2" /> - </test> - </tests> - <help> - -Randomly sample sites from an input VCF dataset. Scale the sampling probability by the field specified by --scale-by (see advanced controls). This may be -used to provide uniform sampling across allele frequencies, for instance (AF field in this case). - -Options:: - - -r, --rate RATE base sampling probability per locus - -s, --scale-by KEY scale sampling likelihood by this Float info field - -p, --random-seed N use this random seed - ----- - -Vcfrandomsample @IS_PART_OF_VCFLIB@ -</help> - <expand macro="citations" /> -</tool> +<tool id="vcfrandomsample" name="VCFrandomSample:" version="@WRAPPER_VERSION@.0"> + <description>Randomly sample sites from VCF dataset</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio" /> + <command> + vcfrandomsample + #if $adv_options.adv_options_selector == "use_adv_controls": + -s "${adv_options.scale_by}" + #end if + -p ${random_seed} + -r ${rate} + "${vcf_input}" > "${out_file1}" + </command> + <inputs> + <param format="vcf" name="vcf_input" type="data" label="Select random sites from"/> + <param name="rate" type="float" value="0.1" label="base sampling probability per locus" help="-r, --rate"/> + <param name="random_seed" type="integer" value="17823618326" label="use this random seed" + help="-p, --random-seed; use this to make results reproducible" /> + <conditional name="adv_options"> + <param name="adv_options_selector" type="select" label="Advanced controls" help="Allows you to specify options that are not listed above"> + <option value="no">Don't use advanced options</option> + <option value="use_adv_controls">Use advanced options</option> + </param> + <when value="" /> + <when value="use_adv_controls"> + <param name="scale_by" type="text" value="AF" label="scale sampling likelihood by this INFO field" help="-s, --scale-by; this only works for Float info fields such as AF" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="vcf" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="vcf_input" value="vcflib.vcf"/> + <param name="rate" value="0.2" /> + <param name="random_seed" value="1" /> + <param name="adv_options_selector" value="no" /> + <output name="out_file1" file="vcfrandomsample-test1.vcf" lines_diff="2" /> + </test> + </tests> + <help> + +Randomly sample sites from an input VCF dataset. Scale the sampling probability by the field specified by --scale-by (see advanced controls). This may be +used to provide uniform sampling across allele frequencies, for instance (AF field in this case). + +---- + +Vcfrandomsample @IS_PART_OF_VCFLIB@ + </help> + <expand macro="citations" /> +</tool>