Mercurial > repos > iuc > bcftools_consensus
comparison bcftools_consensus.xml @ 11:a87ae767b01d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3c56c04b42c70a072429e4534a136dc28c98b642"
author | iuc |
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date | Wed, 23 Oct 2019 19:30:14 -0400 |
parents | 70b8e9908ea8 |
children | e522022137f6 |
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10:f867422772d6 | 11:a87ae767b01d |
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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> |