Mercurial > repos > iuc > crossmap_vcf

annotate crossmap_vcf.xml @ 0:734eedede47c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
author iuc
date Tue, 26 Sep 2017 05:45:41 -0400
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children a40d9af7d058
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734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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1 <tool id="crossmap_vcf" name="CrossMap VCF" version="@WRAPPER_VERSION@-0">
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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3 <macros>
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iuc
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4 <import>macros.xml</import>
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
iuc
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5 </macros>
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iuc
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6 <expand macro="requirements"/>
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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7 <expand macro="stdio"/>
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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8 <expand macro="version_command"/>
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9
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10 <command><![CDATA[
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11 #set $input_file = str($seq_source.input)
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13 CrossMap.py
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14 vcf
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16 #if $seq_source.index_source == "cached"
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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17 <!-- This is the 2nd dbkey, and the corresponding value has to be looked up -->
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18 "${filter(lambda x: str( x[1] ) == str($chain_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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19 #else
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20 "$chain_source.input_chain"
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21 #end if
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23 '${input_file}'
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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24 '${seq_source.input_fasta}'
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26 '${output}'
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27
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28 && mv "${output}.unmap" "$output_unmapped"
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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29 ]]></command>
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31 <inputs>
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32 <conditional name="seq_source">
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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33 <expand macro="source" />
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34
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35 <when value="cached">
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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36 <param type="data" format="vcf" name="input" label="VCF file">
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37 <validator type="unspecified_build"/>
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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38 <!-- Gives error in tests
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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."/>
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40 -->
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41 </param>
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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42 <!-- automatically fetch a FASTA file from the same DBKEY as the chain file -->
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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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">
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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44 <options from_file="all_fasta.loc">
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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45 <column name="name" index="2"/>
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46 <column name="value" index="3"/>
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47 <column name="dbkey" index="1"/>
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48 <filter type="param_value" ref="input_chain" column="1"/>
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49 </options>
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50 </param>
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51 </when>
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52
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53 <when value="history">
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54 <param type="data" format="vcf" name="input" label="VCF file"/>
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55 <param type="data" format="fasta" name="input_fasta" multiple="false" label="Full genome FASTA file"/>
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56 </when>
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57 </conditional>
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58 <expand macro="chain" />
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59
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60 </inputs>
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61
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62 <outputs>
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63 <data format="vcf" name="output" label="${tool.name} on ${on_string}" />
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64 <data format="vcf" name="output_unmapped" label="${tool.name} (unmapped) on ${on_string}" />
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65 </outputs>
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66
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67 <tests>
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68 <!-- VCF -->
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69 <test>
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70 <param name="index_source" value="history_all"/>
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71 <param name="input" value="test_vcf_01_input.vcf" ftype="vcf"/>
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72 <param name="input_chain" value="test_vcf_01.over.chain" ftype="csv"/>
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73 <param name="input_fasta" value="test_vcf_01.fasta" ftype="fasta"/>
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74 <param name="include_fails" value="False"/>
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75
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76 <output name="output">
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77 <assert_contents>
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78 <has_text text="##fileformat=VCFv4.2"/>
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79 <has_text text="##liftOverProgram=CrossMap(https://sourceforge.net/projects/crossmap/)"/>
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80 <has_text text="##new_reference_genome="/>
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81 <has_text text="#CHROM"/>
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82 <has_text_matching expression="2.*?rs11449.*?PASS"/>
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83 <has_text_matching expression="2.*?rs84825.*?PASS"/>
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84 <has_text_matching expression="2.*?rs84823.*?PASS"/>
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85 </assert_contents>
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86 </output>
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87 <output name="output_unmapped" file="test_vcf_01_output.vcf.unmap"/>
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88 </test>
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89 </tests>
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90 <help><![CDATA[
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91 @HELP_GENERAL@
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92
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93 VCF
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94 ---
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95
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96 VCF (variant call format) is a flexible and extendable line-oriented
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97 text format developed by the 1000 Genome Project. It is useful for
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98 representing single nucleotide variants, indels, copy number
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99 variants, and structural variants. Chromosomes, coordinates, and
734eedede47c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit d578fad97ce545d68dde40155d36426a121e4447
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100 reference alleles are updated to a new assembly, and all the other
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101 fields are not changed.
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102
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103 NOTE:
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104
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105 - Genome coordinates and reference allele will be updated to target assembly.
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106 - Reference genome is genome sequence of target assembly.
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107 - If the reference genome sequence file (../database/genome/hg18.fa) was
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108 not indexed, CrossMap will automatically indexed it (only the first time
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109 you run CrossMap).
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110 - In the output VCF file, whether the chromosome IDs contain “chr” or not
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111 depends on the format of the input VCF file.
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112
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113 Please see `the manual <http://crossmap.sourceforge.net/#convert-vcf-format-files>`__ for more details
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114 ]]></help>
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115
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116 <citations>
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117 <citation type="doi">10.1093/bioinformatics/btt730</citation>
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118 </citations>
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119 </tool>