Mercurial > repos > iuc > crossmap_vcf

comparison crossmap_vcf.xml @ 7:71730c177cdf draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
author iuc
date Thu, 15 Jul 2021 16:20:06 +0000
parents 9d61d74f03a4
children 6e96c77f5824
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6:b21851ddcc79 7:71730c177cdf
1 <tool id="crossmap_vcf" name="CrossMap VCF" version="@WRAPPER_VERSION@"> 1 <tool id="crossmap_vcf" name="CrossMap VCF" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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"/>
19 '${seq_source.chain_source.input_chain}' 19 '${seq_source.chain_source.input_chain}'
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 $no_comp_alleles
25 output 25 output
26 ]]></command> 26 ]]></command>
27 27
28 <inputs> 28 <inputs>
29 <conditional name="seq_source"> 29 <conditional name="seq_source">
52 <param name="input_fasta" type="data" format="fasta" label="Full genome FASTA file"/> 52 <param name="input_fasta" type="data" format="fasta" label="Full genome FASTA file"/>
53 53
54 <expand macro="chain" /> 54 <expand macro="chain" />
55 </when> 55 </when>
56 </conditional> 56 </conditional>
57 <param argument="--no-comp-alleles" type="boolean" truevalue="" falsevalue="--no-comp-alleles" checked="true" label="Check if the reference allele is different from the alternate allele"/>
57 </inputs> 58 </inputs>
58 59
59 <outputs> 60 <outputs>
60 <data name="output" format="vcf" label="${tool.name} on ${on_string}" from_work_dir="output" /> 61 <data name="output" format="vcf" label="${tool.name} on ${on_string}" from_work_dir="output" />
61 <data name="output_unmapped" format="vcf" label="${tool.name} (unmapped) on ${on_string}" from_work_dir="output.unmap" /> 62 <data name="output_unmapped" format="vcf" label="${tool.name} (unmapped) on ${on_string}" from_work_dir="output.unmap" />
70 <param name="input_chain" value="test_vcf_01.over.chain" ftype="csv"/> 71 <param name="input_chain" value="test_vcf_01.over.chain" ftype="csv"/>
71 72
72 <output name="output"> 73 <output name="output">
73 <assert_contents> 74 <assert_contents>
74 <has_text text="##fileformat=VCFv4.2"/> 75 <has_text text="##fileformat=VCFv4.2"/>
75 <has_text text="##liftOverProgram=CrossMap(https://sourceforge.net/projects/crossmap/)"/> 76 <has_text_matching expression="##liftOverProgram=&lt;CrossMap,version=[0-9.]+,website=https://sourceforge.net/projects/crossmap&gt;"/>
76 <has_text text="##new_reference_genome="/> 77 <has_text text="##targetRefGenome="/>
77 <has_text text="#CHROM"/> 78 <has_text text="#CHROM"/>
78 <has_text_matching expression="2.*?rs11449.*?PASS"/> 79 <has_text_matching expression="2.*?rs11449.*?PASS"/>
79 <has_text_matching expression="2.*?rs84825.*?PASS"/> 80 <has_text_matching expression="2.*?rs84825.*?PASS"/>
80 </assert_contents> 81 </assert_contents>
81 </output> 82 </output>