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comparison crossmap_vcf.xml @ 3:9db73ff23c9f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622
author iuc
date Thu, 24 May 2018 19:09:50 -0400
parents 7a3c34157901
children 9d61d74f03a4
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2:7a3c34157901 3:9db73ff23c9f
1 <tool id="crossmap_vcf" name="CrossMap VCF" version="@WRAPPER_VERSION@-0"> 1 <tool id="crossmap_vcf" name="CrossMap VCF" version="@WRAPPER_VERSION@">
2 <description>Convert genome coordinates or annotation files between genome assemblies</description> 2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
20 #end if 20 #end if
21 21
22 '${input_file}' 22 '${input_file}'
23 '${seq_source.input_fasta}' 23 '${seq_source.input_fasta}'
24 24
25 '${output}' 25 output
26
27 && mv '${output}.unmap' '$output_unmapped'
28 ]]></command> 26 ]]></command>
29 27
30 <inputs> 28 <inputs>
31 <conditional name="seq_source"> 29 <conditional name="seq_source">
32 <param name="index_source_s" type="select" label="Source for Input Data"> 30 <param name="index_source_s" type="select" label="Source for Input Data">
57 </when> 55 </when>
58 </conditional> 56 </conditional>
59 </inputs> 57 </inputs>
60 58
61 <outputs> 59 <outputs>
62 <data name="output" format="vcf" label="${tool.name} on ${on_string}" /> 60 <data name="output" format="vcf" label="${tool.name} on ${on_string}" from_work_dir="output" />
63 <data name="output_unmapped" format="vcf" label="${tool.name} (unmapped) on ${on_string}" /> 61 <data name="output_unmapped" format="vcf" label="${tool.name} (unmapped) on ${on_string}" from_work_dir="output.unmap" />
64 </outputs> 62 </outputs>
65 63
66 <tests> 64 <tests>
67 <test> 65 <test>
68 <param name="index_source_s" value="history"/> 66 <param name="index_source_s" value="history"/>
105 - If the reference genome sequence file (../database/genome/hg18.fa) was 103 - If the reference genome sequence file (../database/genome/hg18.fa) was
106 not indexed, CrossMap will automatically indexed it (only the first time 104 not indexed, CrossMap will automatically indexed it (only the first time
107 you run CrossMap). 105 you run CrossMap).
108 - In the output VCF file, whether the chromosome IDs contain “chr” or not 106 - In the output VCF file, whether the chromosome IDs contain “chr” or not
109 depends on the format of the input VCF file. 107 depends on the format of the input VCF file.
110
111 ]]></help> 108 ]]></help>
112 109
113 <citations> 110 <citations>
114 <citation type="doi">10.1093/bioinformatics/btt730</citation> 111 <citation type="doi">10.1093/bioinformatics/btt730</citation>
115 </citations> 112 </citations>