Mercurial > repos > iuc > bcftools_consensus

comparison bcftools_consensus.xml @ 9:130789161fcc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
author iuc
date Wed, 05 Jun 2019 12:36:34 -0400
parents f31c7695a6e5
children 91c3ed51093d
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8:f31c7695a6e5 9:130789161fcc
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1">
3 <description>Create consensus sequence by applying VCF variants to a reference fasta file</description> 3 <description>Create consensus sequence by applying VCF variants to a reference fasta file</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">consensus</token> 5 <token name="@EXECUTABLE@">consensus</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
10 </expand> 10 </expand>
11 <expand macro="version_command" /> 11 <expand macro="version_command" />
12 <command detect_errors="aggressive"><![CDATA[ 12 <command detect_errors="aggressive"><![CDATA[
13 @PREPARE_ENV@ 13 @PREPARE_ENV@
14 @PREPARE_INPUT_FILE@ 14 @PREPARE_INPUT_FILE@
15 #set $section = $sec_default 15 #set $section = $reference_source
16 @PREPARE_FASTA_REF@ 16 @PREPARE_FASTA_REF@
17 17
18 bcftools @EXECUTABLE@ 18 bcftools @EXECUTABLE@
19 19
20 @FASTA_REF@
21
20 ## Default section 22 ## Default section
21 #set $section = $sec_default 23 #set $section = $sec_default
22 @FASTA_REF@
23 24
24 ${section.iupac_codes} 25 ${section.iupac_codes}
25 26
26 #if $section.mask: 27 #if $section.mask:
27 --mask "${section.mask}" 28 --mask "${section.mask}"
41 @INPUT_FILE@ 42 @INPUT_FILE@
42 ]]> 43 ]]>
43 </command> 44 </command>
44 <inputs> 45 <inputs>
45 <expand macro="macro_input" /> 46 <expand macro="macro_input" />
47 <expand macro="macro_fasta_ref" />
46 <section name="sec_default" expanded="true" title="Default Options"> 48 <section name="sec_default" expanded="true" title="Default Options">
47 <expand macro="macro_fasta_ref" />
48 <param name="mask" type="data" format="tabular" label="Mask" optional="True" help="Replace regions with N" /> 49 <param name="mask" type="data" format="tabular" label="Mask" optional="True" help="Replace regions with N" />
49
50 <param name="iupac_codes" type="boolean" truevalue="--iupac-codes" falsevalue="" label="Iupac Codes" 50 <param name="iupac_codes" type="boolean" truevalue="--iupac-codes" falsevalue="" label="Iupac Codes"
51 help="Output variants in the form of IUPAC ambiguity codes" /> 51 help="Output variants in the form of IUPAC ambiguity codes" />
52 <expand macro="macro_sample" /> 52 <expand macro="macro_sample" />
53 <param name="select_haplotype" type="select" optional="true"> 53 <param name="select_haplotype" type="select" optional="true">
54 <option value="1">1</option> 54 <option value="1">1</option>
63 <filter>chain</filter> 63 <filter>chain</filter>
64 </data> 64 </data>
65 </outputs> 65 </outputs>
66 <tests> 66 <tests>
67 <test> 67 <test>
68 <param name="fasta_ref" ftype="fasta" value="consensus.fa" /> 68 <expand macro="test_using_reference" ref="consensus.fa" />
69 <param name="input_file" ftype="vcf" value="consensus.vcf" /> 69 <param name="input_file" ftype="vcf" value="consensus.vcf" />
70 <param name="mask" ftype="tabular" value="consensus.tab" />
71 <param name="chain" value="True" />
72 <output name="output_file">
73 <assert_contents>
74 <has_text text="NNNNNNNNNNNNNNNNNNNNNNNNNN" />
75 </assert_contents>
76 </output>
77 <output name="chain_file">
78 <assert_contents>
79 <has_text text="chain 497 1 501 + 1 501 1 502 + 1 502 1" />
80 </assert_contents>
81 </output>
82 </test>
83 <test>
84 <expand macro="test_using_reference" select_from="cached" ref="consensus" />
85 <param name="input_file" ftype="vcf" dbkey="?" value="consensus.vcf" />
70 <param name="mask" ftype="tabular" value="consensus.tab" /> 86 <param name="mask" ftype="tabular" value="consensus.tab" />
71 <param name="chain" value="True" /> 87 <param name="chain" value="True" />
72 <output name="output_file"> 88 <output name="output_file">
73 <assert_contents> 89 <assert_contents>
74 <has_text text="NNNNNNNNNNNNNNNNNNNNNNNNNN" /> 90 <has_text text="NNNNNNNNNNNNNNNNNNNNNNNNNN" />