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comparison crossmap_vcf.xml @ 0:734eedede47c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
author iuc
date Tue, 26 Sep 2017 05:45:41 -0400
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1 <tool id="crossmap_vcf" name="CrossMap VCF" version="@WRAPPER_VERSION@-0">
2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9
10 <command><![CDATA[
11 #set $input_file = str($seq_source.input)
12
13 CrossMap.py
14 vcf
15
16 #if $seq_source.index_source == "cached"
17 <!-- This is the 2nd dbkey, and the corresponding value has to be looked up -->
18 "${filter(lambda x: str( x[1] ) == str($chain_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
19 #else
20 "$chain_source.input_chain"
21 #end if
22
23 '${input_file}'
24 '${seq_source.input_fasta}'
25
26 '${output}'
27
28 && mv "${output}.unmap" "$output_unmapped"
29 ]]></command>
30
31 <inputs>
32 <conditional name="seq_source">
33 <expand macro="source" />
34
35 <when value="cached">
36 <param type="data" format="vcf" name="input" label="VCF file">
37 <validator type="unspecified_build"/>
38 <!-- Gives error in tests
39 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build."/>
40 -->
41 </param>
42 <!-- automatically fetch a FASTA file from the same DBKEY as the chain file -->
43 <param name="input_fasta" type="select" label="Lift Over To (FASTA file)" help="The FASTA file must be on the same build (dbkey) as the LiftOver chain file">
44 <options from_file="all_fasta.loc">
45 <column name="name" index="2"/>
46 <column name="value" index="3"/>
47 <column name="dbkey" index="1"/>
48 <filter type="param_value" ref="input_chain" column="1"/>
49 </options>
50 </param>
51 </when>
52
53 <when value="history">
54 <param type="data" format="vcf" name="input" label="VCF file"/>
55 <param type="data" format="fasta" name="input_fasta" multiple="false" label="Full genome FASTA file"/>
56 </when>
57 </conditional>
58 <expand macro="chain" />
59
60 </inputs>
61
62 <outputs>
63 <data format="vcf" name="output" label="${tool.name} on ${on_string}" />
64 <data format="vcf" name="output_unmapped" label="${tool.name} (unmapped) on ${on_string}" />
65 </outputs>
66
67 <tests>
68 <!-- VCF -->
69 <test>
70 <param name="index_source" value="history_all"/>
71 <param name="input" value="test_vcf_01_input.vcf" ftype="vcf"/>
72 <param name="input_chain" value="test_vcf_01.over.chain" ftype="csv"/>
73 <param name="input_fasta" value="test_vcf_01.fasta" ftype="fasta"/>
74 <param name="include_fails" value="False"/>
75
76 <output name="output">
77 <assert_contents>
78 <has_text text="##fileformat=VCFv4.2"/>
79 <has_text text="##liftOverProgram=CrossMap(https://sourceforge.net/projects/crossmap/)"/>
80 <has_text text="##new_reference_genome="/>
81 <has_text text="#CHROM"/>
82 <has_text_matching expression="2.*?rs11449.*?PASS"/>
83 <has_text_matching expression="2.*?rs84825.*?PASS"/>
84 <has_text_matching expression="2.*?rs84823.*?PASS"/>
85 </assert_contents>
86 </output>
87 <output name="output_unmapped" file="test_vcf_01_output.vcf.unmap"/>
88 </test>
89 </tests>
90 <help><![CDATA[
91 @HELP_GENERAL@
92
93 VCF
94 ---
95
96 VCF (variant call format) is a flexible and extendable line-oriented
97 text format developed by the 1000 Genome Project. It is useful for
98 representing single nucleotide variants, indels, copy number
99 variants, and structural variants. Chromosomes, coordinates, and
100 reference alleles are updated to a new assembly, and all the other
101 fields are not changed.
102
103 NOTE:
104
105 - Genome coordinates and reference allele will be updated to target assembly.
106 - Reference genome is genome sequence of target assembly.
107 - If the reference genome sequence file (../database/genome/hg18.fa) was
108 not indexed, CrossMap will automatically indexed it (only the first time
109 you run CrossMap).
110 - In the output VCF file, whether the chromosome IDs contain “chr” or not
111 depends on the format of the input VCF file.
112
113 Please see `the manual <http://crossmap.sourceforge.net/#convert-vcf-format-files>`__ for more details
114 ]]></help>
115
116 <citations>
117 <citation type="doi">10.1093/bioinformatics/btt730</citation>
118 </citations>
119 </tool>