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comparison crossmap_vcf.xml @ 10:d4965adac10c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
author iuc
date Mon, 02 Sep 2024 12:01:12 +0000
parents 6e96c77f5824
children
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9:18f7e96459d2 10:d4965adac10c
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
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
10 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
11 #set $input_file = str($seq_source.input) 10 #set $input_file = str($seq_source.input)
12 11
13 ln -s '${seq_source.input_fasta}' 'genome.fasta' && 12 ln -s '${seq_source.input_fasta}' 'genome.fasta' &&
14 13
15 CrossMap.py vcf 14 CrossMap vcf
16 15
17 #if $seq_source.index_source_s == "cached" 16 #if $seq_source.index_source_s == "cached"
18 ## This is the 2nd dbkey, and the corresponding value has to be looked up 17 ## This is the 2nd dbkey, and the corresponding value has to be looked up
19 "${filter(lambda x: str( x[1] ) == str($seq_source.chain_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }" 18 "${filter(lambda x: str( x[1] ) == str($seq_source.chain_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
20 #else 19 #else
24 '${input_file}' 23 '${input_file}'
25 'genome.fasta' 24 'genome.fasta'
26 $no_comp_alleles 25 $no_comp_alleles
27 output 26 output
28 ]]></command> 27 ]]></command>
29
30 <inputs> 28 <inputs>
31 <conditional name="seq_source"> 29 <conditional name="seq_source">
32 <param name="index_source_s" type="select" label="Source for Input Data"> 30 <param name="index_source_s" type="select" label="Source for Input Data">
33 <option value="cached">Local data (in galaxy)</option> 31 <option value="cached">Local data (in galaxy)</option>
34 <option value="history">From History</option> 32 <option value="history">From History</option>
43 --> 41 -->
44 </param> 42 </param>
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"> 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">
46 <options from_data_table="all_fasta"/> 44 <options from_data_table="all_fasta"/>
47 </param> 45 </param>
48 46 <expand macro="chain"/>
49 <expand macro="chain" />
50 </when> 47 </when>
51
52 <when value="history"> 48 <when value="history">
53 <param name="input" type="data" format="vcf" label="VCF file"/> 49 <param name="input" type="data" format="vcf" label="VCF file"/>
54 <param name="input_fasta" type="data" format="fasta" label="Full genome FASTA file"/> 50 <param name="input_fasta" type="data" format="fasta" label="Full genome FASTA file"/>
55 51 <expand macro="chain"/>
56 <expand macro="chain" />
57 </when> 52 </when>
58 </conditional> 53 </conditional>
59 <param argument="--no-comp-alleles" type="boolean" truevalue="" falsevalue="--no-comp-alleles" checked="true" label="Check if the reference allele is different from the alternate allele"/> 54 <param argument="--no-comp-alleles" type="boolean" truevalue="" falsevalue="--no-comp-alleles" checked="true" label="Check if the reference allele is different from the alternate allele"/>
60 </inputs> 55 </inputs>
61
62 <outputs> 56 <outputs>
63 <data name="output" format="vcf" label="${tool.name} on ${on_string}" from_work_dir="output" /> 57 <data name="output" format="vcf" label="${tool.name} on ${on_string}" from_work_dir="output"/>
64 <data name="output_unmapped" format="vcf" label="${tool.name} (unmapped) on ${on_string}" from_work_dir="output.unmap" /> 58 <data name="output_unmapped" format="vcf" label="${tool.name} (unmapped) on ${on_string}" from_work_dir="output.unmap"/>
65 </outputs> 59 </outputs>
66
67 <tests> 60 <tests>
68 <test> 61 <test>
69 <param name="index_source_s" value="history"/> 62 <param name="index_source_s" value="history"/>
70 <param name="input" value="test_vcf_01_input.vcf" ftype="vcf"/> 63 <param name="input" value="test_vcf_01_input.vcf" ftype="vcf"/>
71 <param name="index_source" value="history"/> 64 <param name="index_source" value="history"/>
72 <param name="input_fasta" value="test_vcf_01.fasta" ftype="fasta"/> 65 <param name="input_fasta" value="test_vcf_01.fasta" ftype="fasta"/>
73 <param name="input_chain" value="test_vcf_01.over.chain" ftype="csv"/> 66 <param name="input_chain" value="test_vcf_01.over.chain" ftype="csv"/>
74
75 <output name="output"> 67 <output name="output">
76 <assert_contents> 68 <assert_contents>
77 <has_text text="##fileformat=VCFv4.2"/> 69 <has_text text="##fileformat=VCFv4.2"/>
78 <has_text_matching expression="##liftOverProgram=&lt;CrossMap,version=[0-9.]+,website=https://sourceforge.net/projects/crossmap&gt;"/> 70 <has_text_matching expression="##liftOverProgram=CrossMap,version=[0-9.]+,website=https://crossmap.readthedocs.io/en/latest"/>
79 <has_text text="##targetRefGenome="/> 71 <has_text text="##targetRefGenome="/>
80 <has_text text="#CHROM"/> 72 <has_text text="#CHROM"/>
81 <has_text_matching expression="2.*?rs11449.*?PASS"/> 73 <has_text_matching expression="2.*?rs11449.*?PASS"/>
82 <has_text_matching expression="2.*?rs84825.*?PASS"/> 74 <has_text_matching expression="2.*?rs84825.*?PASS"/>
83 </assert_contents> 75 </assert_contents>
106 not indexed, CrossMap will automatically indexed it (only the first time 98 not indexed, CrossMap will automatically indexed it (only the first time
107 you run CrossMap). 99 you run CrossMap).
108 - In the output VCF file, whether the chromosome IDs contain “chr” or not 100 - In the output VCF file, whether the chromosome IDs contain “chr” or not
109 depends on the format of the input VCF file. 101 depends on the format of the input VCF file.
110 ]]></help> 102 ]]></help>
111
112 <citations> 103 <citations>
113 <citation type="doi">10.1093/bioinformatics/btt730</citation> 104 <citation type="doi">10.1093/bioinformatics/btt730</citation>
114 </citations> 105 </citations>
115 </tool> 106 </tool>