Mercurial > repos > jjohnson > bcftools_filter
changeset 1:201536a80600 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 15:34:31 -0400 |
| parents | 442f9d982db3 |
| children | |
| files | bcftools_consensus.xml bcftools_filter.xml test-data/fixploidy.ploidy test-data/fixploidy.samples |
| diffstat | 4 files changed, 109 insertions(+), 13 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bcftools_consensus.xml Sun Jun 26 15:34:31 2016 -0400 @@ -0,0 +1,96 @@ +<?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>
--- a/bcftools_filter.xml Sat Jun 25 20:47:47 2016 -0400 +++ b/bcftools_filter.xml Sun Jun 26 15:34:31 2016 -0400 @@ -165,7 +165,7 @@ <param name="input_file" ftype="vcf" value="filter.3.vcf" /> <param name="exclude" value="DP=19" /> <param name="soft_filter" value="XX" /> - <param name="mode" value="\+x" /> + <param name="mode" value="+x" /> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents>
--- a/test-data/fixploidy.ploidy Sat Jun 25 20:47:47 2016 -0400 +++ b/test-data/fixploidy.ploidy Sun Jun 26 15:34:31 2016 -0400 @@ -1,9 +1,9 @@ -1 3000001 3000001 X 0 -1 3000001 3000001 Y 1 -1 3000001 3000001 Z 2 -1 3000002 3000002 X 3 -1 3000002 3000002 Y 4 -1 3000002 3000002 Z 5 -1 3000004 3000004 X 6 -1 3000004 3000004 Y 7 -1 3000004 3000004 Z 8 +1 3000001 3000001 X 0 +1 3000001 3000001 Y 1 +1 3000001 3000001 Z 2 +1 3000002 3000002 X 3 +1 3000002 3000002 Y 4 +1 3000002 3000002 Z 5 +1 3000004 3000004 X 6 +1 3000004 3000004 Y 7 +1 3000004 3000004 Z 8