Mercurial > repos > iuc > bcftools_consensus
diff bcftools_consensus.xml @ 8:70b8e9908ea8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
author | iuc |
---|---|
date | Wed, 05 Jun 2019 12:58:42 -0400 |
parents | 2363ef414c9b |
children | a87ae767b01d |
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--- a/bcftools_consensus.xml Thu Feb 21 15:54:32 2019 -0500 +++ b/bcftools_consensus.xml Wed Jun 05 12:58:42 2019 -0400 @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='utf-8'?> -<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@"> +<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1"> <description>Create consensus sequence by applying VCF variants to a reference fasta file</description> <macros> <token name="@EXECUTABLE@">consensus</token> @@ -12,14 +12,15 @@ <command detect_errors="aggressive"><![CDATA[ @PREPARE_ENV@ @PREPARE_INPUT_FILE@ -#set $section = $sec_default +#set $section = $reference_source @PREPARE_FASTA_REF@ bcftools @EXECUTABLE@ +@FASTA_REF@ + ## Default section #set $section = $sec_default -@FASTA_REF@ ${section.iupac_codes} @@ -43,10 +44,9 @@ </command> <inputs> <expand macro="macro_input" /> + <expand macro="macro_fasta_ref" /> <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" /> @@ -65,7 +65,7 @@ </outputs> <tests> <test> - <param name="fasta_ref" ftype="fasta" value="consensus.fa" /> + <expand macro="test_using_reference" ref="consensus.fa" /> <param name="input_file" ftype="vcf" value="consensus.vcf" /> <param name="mask" ftype="tabular" value="consensus.tab" /> <param name="chain" value="True" /> @@ -80,6 +80,22 @@ </assert_contents> </output> </test> + <test> + <expand macro="test_using_reference" select_from="cached" ref="consensus" /> + <param name="input_file" ftype="vcf" dbkey="?" 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> + </test> </tests> <help><![CDATA[ =====================================