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comparison crossmap_vcf.xml @ 1:a40d9af7d058 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
author iuc
date Fri, 20 Oct 2017 02:51:15 -0400
parents 734eedede47c
children 7a3c34157901
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0:734eedede47c 1:a40d9af7d058
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 9
10 <command><![CDATA[ 10 <command><![CDATA[
11 #set $input_file = str($seq_source.input) 11 #set $input_file = str($seq_source.input)
12 12
13 CrossMap.py 13 CrossMap.py vcf
14 vcf
15 14
16 #if $seq_source.index_source == "cached" 15 #if $seq_source.index_source_s == "cached"
17 <!-- This is the 2nd dbkey, and the corresponding value has to be looked up --> 16 ## This is the 2nd dbkey, and the corresponding value has to be looked up
18 "${filter(lambda x: str( x[1] ) == str($chain_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }" 17 "${filter(lambda x: str( x[1] ) == str($chain_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
19 #else 18 #else
20 "$chain_source.input_chain" 19 '${chain_source.input_chain}'
21 #end if 20 #end if
22 21
23 '${input_file}' 22 '${input_file}'
24 '${seq_source.input_fasta}' 23 '${seq_source.input_fasta}'
25 24
26 '${output}' 25 '${output}'
27 26
28 && mv "${output}.unmap" "$output_unmapped" 27 && mv '${output}.unmap' '$output_unmapped'
29 ]]></command> 28 ]]></command>
30 29
31 <inputs> 30 <inputs>
32 <conditional name="seq_source"> 31 <conditional name="seq_source">
33 <expand macro="source" /> 32 <param name="index_source_s" type="select" label="Source for Input Data">
34 33 <option value="cached">Local data (in galaxy)</option>
34 <option value="history">From History</option>
35 </param>
35 <when value="cached"> 36 <when value="cached">
36 <param type="data" format="vcf" name="input" label="VCF file"> 37 <param name="input" type="data" format="vcf" label="VCF file">
38 <!--
37 <validator type="unspecified_build"/> 39 <validator type="unspecified_build"/>
40 -->
38 <!-- Gives error in tests 41 <!-- 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."/> 42 <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 --> 43 -->
41 </param> 44 </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"> 45 <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"> 46 <options from_data_table="all_fasta"/>
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> 47 </param>
51 </when> 48 </when>
52 49
53 <when value="history"> 50 <when value="history">
54 <param type="data" format="vcf" name="input" label="VCF file"/> 51 <param name="input" type="data" format="vcf" label="VCF file"/>
55 <param type="data" format="fasta" name="input_fasta" multiple="false" label="Full genome FASTA file"/> 52 <param name="input_fasta" type="data" format="fasta" label="Full genome FASTA file"/>
56 </when> 53 </when>
57 </conditional> 54 </conditional>
58 <expand macro="chain" /> 55 <expand macro="chain" />
59
60 </inputs> 56 </inputs>
61 57
62 <outputs> 58 <outputs>
63 <data format="vcf" name="output" label="${tool.name} on ${on_string}" /> 59 <data name="output" format="vcf" label="${tool.name} on ${on_string}" />
64 <data format="vcf" name="output_unmapped" label="${tool.name} (unmapped) on ${on_string}" /> 60 <data name="output_unmapped" format="vcf" label="${tool.name} (unmapped) on ${on_string}" />
65 </outputs> 61 </outputs>
66 62
67 <tests> 63 <tests>
68 <!-- VCF -->
69 <test> 64 <test>
70 <param name="index_source" value="history_all"/> 65 <param name="index_source_s" value="history"/>
71 <param name="input" value="test_vcf_01_input.vcf" ftype="vcf"/> 66 <param name="input" value="test_vcf_01_input.vcf" ftype="vcf"/>
67 <param name="index_source" value="history"/>
68 <param name="input_fasta" value="test_vcf_01.fasta" ftype="fasta"/>
72 <param name="input_chain" value="test_vcf_01.over.chain" ftype="csv"/> 69 <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 70
76 <output name="output"> 71 <output name="output">
77 <assert_contents> 72 <assert_contents>
78 <has_text text="##fileformat=VCFv4.2"/> 73 <has_text text="##fileformat=VCFv4.2"/>
79 <has_text text="##liftOverProgram=CrossMap(https://sourceforge.net/projects/crossmap/)"/> 74 <has_text text="##liftOverProgram=CrossMap(https://sourceforge.net/projects/crossmap/)"/>
91 @HELP_GENERAL@ 86 @HELP_GENERAL@
92 87
93 VCF 88 VCF
94 --- 89 ---
95 90
96 VCF (variant call format) is a flexible and extendable line-oriented 91 VCF (variant call format) is a flexible and extendable line-oriented
97 text format developed by the 1000 Genome Project. It is useful for 92 text format developed by the 1000 Genome Project. It is useful for
98 representing single nucleotide variants, indels, copy number 93 representing single nucleotide variants, indels, copy number
99 variants, and structural variants. Chromosomes, coordinates, and 94 variants, and structural variants. Chromosomes, coordinates, and
100 reference alleles are updated to a new assembly, and all the other 95 reference alleles are updated to a new assembly, and all the other
101 fields are not changed. 96 fields are not changed.
102 97
103 NOTE: 98 Notes:
104 99
105 - Genome coordinates and reference allele will be updated to target assembly. 100 - Genome coordinates and reference allele will be updated to target assembly.
106 - Reference genome is genome sequence of target assembly. 101 - Reference genome is genome sequence of target assembly.
107 - If the reference genome sequence file (../database/genome/hg18.fa) was 102 - If the reference genome sequence file (../database/genome/hg18.fa) was
108 not indexed, CrossMap will automatically indexed it (only the first time 103 not indexed, CrossMap will automatically indexed it (only the first time
109 you run CrossMap). 104 you run CrossMap).
110 - In the output VCF file, whether the chromosome IDs contain “chr” or not 105 - In the output VCF file, whether the chromosome IDs contain “chr” or not
111 depends on the format of the input VCF file. 106 depends on the format of the input VCF file.
112 107
113 Please see `the manual <http://crossmap.sourceforge.net/#convert-vcf-format-files>`__ for more details 108 ]]></help>
114 ]]></help>
115 109
116 <citations> 110 <citations>
117 <citation type="doi">10.1093/bioinformatics/btt730</citation> 111 <citation type="doi">10.1093/bioinformatics/btt730</citation>
118 </citations> 112 </citations>
119 </tool> 113 </tool>