Mercurial > repos > iuc > bcftools_consensus
comparison bcftools_consensus.xml @ 8:70b8e9908ea8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
author | iuc |
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date | Wed, 05 Jun 2019 12:58:42 -0400 |
parents | 2363ef414c9b |
children | a87ae767b01d |
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7:2363ef414c9b | 8:70b8e9908ea8 |
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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@"> | 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" /> |