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comparison bcftools_consensus.xml @ 0:74b27d899b85 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
author iuc
date Wed, 06 Jul 2016 07:02:04 -0400
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children 5410e1408bce
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-1:000000000000 0:74b27d899b85
1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
3 <description>Create consensus sequence by applying VCF variants to a reference fasta file</description>
4 <macros>
5 <token name="@EXECUTABLE@">consensus</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="requirements" />
9 <expand macro="version_command" />
10 <command detect_errors="aggressive"><![CDATA[
11 @PREPARE_ENV@
12 @PREPARE_INPUT_FILE@
13 #set $section = $sec_default
14 @PREPARE_FASTA_REF@
15
16 bcftools @EXECUTABLE@
17
18 ## Default section
19 #set $section = $sec_default
20 @FASTA_REF@
21
22 ${section.iupac_codes}
23
24 #if $section.mask:
25 --mask "${section.mask}"
26 #end if
27
28 #if $section.select_haplotype:
29 --haplotype "${section.select_haplotype}"
30 #end if
31 @SAMPLE@
32
33 #if $chain:
34 --chain "$chain_file"
35 #end if
36
37 ## Primary Input/Outputs
38 --output "$output_file"
39 @INPUT_FILE@
40 ]]>
41 </command>
42 <inputs>
43 <expand macro="macro_input" />
44 <section name="sec_default" expanded="true" title="Default Options">
45 <expand macro="macro_fasta_ref" />
46 <param name="mask" type="data" format="tabular" label="Mask" optional="True" help="Replace regions with N" />
47
48 <param name="iupac_codes" type="boolean" truevalue="--iupac-codes" falsevalue="" label="Iupac Codes"
49 help="Output variants in the form of IUPAC ambiguity codes" />
50 <expand macro="macro_sample" />
51 <param name="select_haplotype" type="select" optional="true">
52 <option value="1">1</option>
53 <option value="2">2</option>
54 </param>
55 </section>
56 <param name="chain" type="boolean" truevalue="yes" falsevalue="no" label="Write a chain file for liftover" />
57 </inputs>
58 <outputs>
59 <data name="output_file" format="fasta" label="${tool.name} on ${on_string}: consensus fasta"/>
60 <data name="chain_file" format="txt" label="${tool.name} on ${on_string}: chain">
61 <filter>chain</filter>
62 </data>
63 </outputs>
64 <tests>
65 <test>
66 <param name="fasta_ref" ftype="fasta" value="consensus.fa" />
67 <param name="input_file" ftype="vcf" value="consensus.vcf" />
68 <param name="mask" ftype="tabular" value="consensus.tab" />
69 <param name="chain" value="True" />
70 <output name="output_file">
71 <assert_contents>
72 <has_text text="NNNNNNNNNNNNNNNNNNNNNNNNNN" />
73 </assert_contents>
74 </output>
75 <output name="chain_file">
76 <assert_contents>
77 <has_text text="chain 497 1 501 + 1 501 1 502 + 1 502 1" />
78 </assert_contents>
79 </output>
80 </test>
81 </tests>
82 <help><![CDATA[
83 =====================================
84 bcftools @EXECUTABLE@ plugin
85 =====================================
86
87
88 Create consensus sequence by applying VCF variants to a reference fasta file.
89
90 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
91
92 @BCFTOOLS_WIKI@
93 ]]>
94 </help>
95 <expand macro="citations" />
96 </tool>