Mercurial > repos > iuc > bcftools_consensus

comparison bcftools_consensus.xml @ 12:91c3ed51093d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3c56c04b42c70a072429e4534a136dc28c98b642"
author iuc
date Wed, 23 Oct 2019 19:09:14 -0400
parents 130789161fcc
children f56a1a62cb12
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11:c4ed8e4032d5 12:91c3ed51093d
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@+galaxy1"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy2">
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>
8 <expand macro="requirements"> 8 <expand macro="requirements">
9 <expand macro="samtools_requirement"/> 9 <expand macro="samtools_requirement"/>
10 <requirement type="package" version="5.0.1">gawk</requirement>
10 </expand> 11 </expand>
11 <expand macro="version_command" /> 12 <expand macro="version_command" />
12 <command detect_errors="aggressive"><![CDATA[ 13 <command detect_errors="aggressive"><![CDATA[
13 @PREPARE_ENV@ 14 @PREPARE_ENV@
14 @PREPARE_INPUT_FILE@ 15 @PREPARE_INPUT_FILE@
23 #set $section = $sec_default 24 #set $section = $sec_default
24 25
25 ${section.iupac_codes} 26 ${section.iupac_codes}
26 27
27 #if $section.mask: 28 #if $section.mask:
28 --mask "${section.mask}" 29 --mask '${section.mask}'
29 #end if 30 #end if
30 31
31 #if $section.select_haplotype: 32 #if $section.select_haplotype:
32 --haplotype "${section.select_haplotype}" 33 --haplotype '${section.select_haplotype}'
33 #end if 34 #end if
34 @SAMPLE@ 35 @SAMPLE@
35 36
36 #if $chain: 37 #if $chain:
37 --chain "$chain_file" 38 --chain '$chain_file'
38 #end if 39 #end if
39 40
40 ## Primary Input/Outputs 41 ## Primary Input/Outputs
41 --output "$output_file" 42 #if str($rename) == "no"
43 --output '$output_file'
44 #end if
42 @INPUT_FILE@ 45 @INPUT_FILE@
46 #if str($rename) == "yes":
47 #set basename=$input_file.element_identifier
48 | awk 'BEGIN {i=1} {if (match($0, /^>/)) {if (i==1) {name="${basename}"} else {name=sprintf("%s-%d","${basename}",i);} print(gensub(/>[^ ]+( ?.*)/, ">" name "\\1", 1)); i=i+1;} else {print}}' > '$output_file'
49 #end if
43 ]]> 50 ]]>
44 </command> 51 </command>
45 <inputs> 52 <inputs>
46 <expand macro="macro_input" /> 53 <expand macro="macro_input" />
47 <expand macro="macro_fasta_ref" /> 54 <expand macro="macro_fasta_ref" />
54 <option value="1">1</option> 61 <option value="1">1</option>
55 <option value="2">2</option> 62 <option value="2">2</option>
56 </param> 63 </param>
57 </section> 64 </section>
58 <param name="chain" type="boolean" truevalue="yes" falsevalue="no" label="Write a chain file for liftover" /> 65 <param name="chain" type="boolean" truevalue="yes" falsevalue="no" label="Write a chain file for liftover" />
66 <param name="rename" type="boolean" truevalue="yes" falsevalue="no" label="Set output FASTA ID from name of VCF" />
59 </inputs> 67 </inputs>
60 <outputs> 68 <outputs>
61 <data name="output_file" format="fasta" label="${tool.name} on ${on_string}: consensus fasta"/> 69 <data name="output_file" format="fasta" label="${tool.name} on ${on_string}: consensus fasta"/>
62 <data name="chain_file" format="txt" label="${tool.name} on ${on_string}: chain"> 70 <data name="chain_file" format="txt" label="${tool.name} on ${on_string}: chain">
63 <filter>chain</filter> 71 <filter>chain</filter>
94 <assert_contents> 102 <assert_contents>
95 <has_text text="chain 497 1 501 + 1 501 1 502 + 1 502 1" /> 103 <has_text text="chain 497 1 501 + 1 501 1 502 + 1 502 1" />
96 </assert_contents> 104 </assert_contents>
97 </output> 105 </output>
98 </test> 106 </test>
107 <test>
108 <expand macro="test_using_reference" ref="consensus.fa" />
109 <param name="input_file" ftype="vcf" value="consensus.vcf" />
110 <param name="mask" ftype="tabular" value="consensus.tab" />
111 <param name="chain" value="False" />
112 <param name="rename" value="True" />
113 <output name="output_file">
114 <assert_contents>
115 <has_text text=">consensus.vcf" />
116 </assert_contents>
117 <assert_contents>
118 <has_text text=">consensus.vcf-2" />
119 </assert_contents>
120 </output>
121 </test>
99 </tests> 122 </tests>
100 <help><![CDATA[ 123 <help><![CDATA[
101 ===================================== 124 =====================================
102 bcftools @EXECUTABLE@ plugin 125 bcftools @EXECUTABLE@ plugin
103 ===================================== 126 =====================================
106 Create consensus sequence by applying VCF variants to a reference fasta file. 129 Create consensus sequence by applying VCF variants to a reference fasta file.
107 130
108 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ 131 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
109 132
110 @BCFTOOLS_WIKI@ 133 @BCFTOOLS_WIKI@
134
135 The option to set the new consensus' FASTA ID from the name of the VCF is provided by post-processing
136 the bcftools consensus output. It is primarily intended for use when the VCF is coming from a list
137 collection where the elements of the list are named meaningfully (e.g. named after sample names). This
138 is useful when consensus sequences are being prepared for, for example, feeding a multiple sequence
139 alignment to a phylogeny program.
111 ]]> 140 ]]>
112 </help> 141 </help>
113 <expand macro="citations" /> 142 <expand macro="citations" />
114 </tool> 143 </tool>