Mercurial > repos > jjohnson > bcftools_call
changeset 2:af912f164fae draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author | jjohnson |
---|---|
date | Sun, 26 Jun 2016 15:46:37 -0400 (2016-06-26) |
parents | 1a4307fecd78 |
children | |
files | bcftools_consensus.xml |
diffstat | 1 files changed, 0 insertions(+), 96 deletions(-) [+] |
line wrap: on
line diff
--- a/bcftools_consensus.xml Sun Jun 26 15:32:19 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,96 +0,0 @@ -<?xml version='1.0' encoding='utf-8'?> -<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0"> - <description>Create consensus sequence by applying VCF variants to a reference fasta file</description> - <macros> - <token name="@EXECUTABLE@">consensus</token> - <import>macros.xml</import> - </macros> - <expand macro="requirements" /> - <expand macro="version_command" /> - <command detect_errors="aggressive"><![CDATA[ -@PREPARE_ENV@ -@PREPARE_INPUT_FILE@ -#set $section = $sec_default -@PREPARE_FASTA_REF@ - -bcftools @EXECUTABLE@ - -## Default section -#set $section = $sec_default -@FASTA_REF@ - -${section.iupac_codes} - -#if $section.mask: - --mask "${section.mask}" -#end if - -#if $section.select_haplotype: - --haplotype "${section.select_haplotype}" -#end if -@SAMPLE@ - -#if $chain: - --chain "$chain_file" -#end if - -## Primary Input/Outputs ---output "$output_file" -@INPUT_FILE@ -]]> - </command> - <inputs> - <expand macro="macro_input" /> - <section name="sec_default" expanded="true" title="Default Options"> - <expand macro="macro_fasta_ref" /> - <param name="mask" type="data" format="tabular" label="Mask" optional="True" help="Replace regions with N" /> - - <param name="iupac_codes" type="boolean" truevalue="--iupac-codes" falsevalue="" label="Iupac Codes" - help="Output variants in the form of IUPAC ambiguity codes" /> - <expand macro="macro_sample" /> - <param name="select_haplotype" type="select" optional="true"> - <option value="1">1</option> - <option value="2">2</option> - </param> - </section> - <param name="chain" type="boolean" truevalue="yes" falsevalue="no" label="Write a chain file for liftover" /> - </inputs> - <outputs> - <data name="output_file" format="fasta" label="${tool.name} on ${on_string}: consensus fasta"/> - <data name="chain_file" format="txt" label="${tool.name} on ${on_string}: chain"> - <filter>chain</filter> - </data> - </outputs> - <tests> - <test> - <param name="reference_fasta" ftype="fasta" value="consensus.fa" /> - <param name="input_file" ftype="vcf" value="consensus.vcf" /> - <param name="mask" ftype="tabular" value="consensus.tab" /> - <param name="chain" value="True" /> - <output name="output_file"> - <assert_contents> - <has_text text="NNNNNNNNNNNNNNNNNNNNNNNNNN" /> - </assert_contents> - </output> - <output name="chain_file"> - <assert_contents> - <has_text text="chain 497 1 501 + 1 501 1 502 + 1 502 1" /> - </assert_contents> - </output> - <output name="chain_file" file="consensus.1.chain" /> - </tests> - <help><![CDATA[ -===================================== - bcftools @EXECUTABLE@ plugin -===================================== - - -Create consensus sequence by applying VCF variants to a reference fasta file. - -@BCFTOOLS_MANPAGE@#@EXECUTABLE@ - -@BCFTOOLS_WIKI@ -]]> - </help> - <expand macro="citations" /> -</tool>