Mercurial > repos > iuc > crossmap_vcf

annotate crossmap_vcf.xml @ 9:30d4d3bbe0a1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 07b2b6b9b288fd4ad368fc7a4f0143bb73e9edd9"
author iuc
date Tue, 16 Nov 2021 19:11:36 +0000
parents 4a9c59111f54
children b17b9f3a148a
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1 <tool id="crossmap_vcf" name="CrossMap VCF" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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10 <command detect_errors="aggressive"><![CDATA[
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11 #set $input_file = str($seq_source.input)
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13 ln -s '${seq_source.input_fasta}' 'genome.fasta' &&
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15 CrossMap.py vcf
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17 #if $seq_source.index_source_s == "cached"
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18 ## This is the 2nd dbkey, and the corresponding value has to be looked up
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19 "${filter(lambda x: str( x[1] ) == str($seq_source.chain_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
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20 #else
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21 '${seq_source.chain_source.input_chain}'
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22 #end if
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23
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24 '${input_file}'
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25 'genome.fasta'
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26 $no_comp_alleles
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27 output
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28 ]]></command>
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30 <inputs>
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31 <conditional name="seq_source">
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32 <param name="index_source_s" type="select" label="Source for Input Data">
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33 <option value="cached">Local data (in galaxy)</option>
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34 <option value="history">From History</option>
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35 </param>
0
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36 <when value="cached">
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37 <param name="input" type="data" format="vcf" label="VCF file">
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38 <!--
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39 <validator type="unspecified_build"/>
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40 -->
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41 <!-- Gives error in tests
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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."/>
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43 -->
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44 </param>
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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">
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46 <options from_data_table="all_fasta"/>
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47 </param>
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48
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49 <expand macro="chain" />
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50 </when>
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51
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52 <when value="history">
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53 <param name="input" type="data" format="vcf" label="VCF file"/>
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54 <param name="input_fasta" type="data" format="fasta" label="Full genome FASTA file"/>
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56 <expand macro="chain" />
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57 </when>
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58 </conditional>
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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"/>
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60 </inputs>
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62 <outputs>
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63 <data name="output" format="vcf" label="${tool.name} on ${on_string}" from_work_dir="output" />
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64 <data name="output_unmapped" format="vcf" label="${tool.name} (unmapped) on ${on_string}" from_work_dir="output.unmap" />
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65 </outputs>
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66
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67 <tests>
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68 <test>
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69 <param name="index_source_s" value="history"/>
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70 <param name="input" value="test_vcf_01_input.vcf" ftype="vcf"/>
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71 <param name="index_source" value="history"/>
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72 <param name="input_fasta" value="test_vcf_01.fasta" ftype="fasta"/>
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73 <param name="input_chain" value="test_vcf_01.over.chain" ftype="csv"/>
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75 <output name="output">
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76 <assert_contents>
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77 <has_text text="##fileformat=VCFv4.2"/>
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78 <has_text_matching expression="##liftOverProgram=&lt;CrossMap,version=[0-9.]+,website=https://sourceforge.net/projects/crossmap&gt;"/>
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79 <has_text text="##targetRefGenome="/>
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80 <has_text text="#CHROM"/>
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81 <has_text_matching expression="2.*?rs11449.*?PASS"/>
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82 <has_text_matching expression="2.*?rs84825.*?PASS"/>
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83 </assert_contents>
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84 </output>
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85 <output name="output_unmapped" file="test_vcf_01_output.vcf.unmap"/>
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86 </test>
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87 </tests>
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88 <help><![CDATA[
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89 @HELP_GENERAL@
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90
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91 VCF
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92 ---
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93
2
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94 VCF (variant call format) is a flexible and extendable line-oriented
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95 text format developed by the 1000 Genome Project. It is useful for
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96 representing single nucleotide variants, indels, copy number
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97 variants, and structural variants. Chromosomes, coordinates, and
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98 reference alleles are updated to a new assembly, and all the other
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99 fields are not changed.
0
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100
2
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101 Notes:
0
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102
2
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103 - Genome coordinates and reference allele will be updated to target assembly.
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104 - Reference genome is genome sequence of target assembly.
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105 - If the reference genome sequence file (../database/genome/hg18.fa) was
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106 not indexed, CrossMap will automatically indexed it (only the first time
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107 you run CrossMap).
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108 - In the output VCF file, whether the chromosome IDs contain “chr” or not
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109 depends on the format of the input VCF file.
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110 ]]></help>
0
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111
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112 <citations>
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113 <citation type="doi">10.1093/bioinformatics/btt730</citation>
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114 </citations>
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115 </tool>