Mercurial > repos > iuc > hgvsparser

annotate hgvsparser.xml @ 0:c12a4d187121 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
author iuc
date Fri, 07 Jun 2024 15:21:07 +0000
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c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
iuc
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1 <tool id="hgvsparser" name="hgvsParseR" version="@VERSION@+galaxy@GALAXY_VERSION@" profile="20.09"
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
iuc
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2 license="GPL-3.0" >
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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3 <description>parsing and building variant descriptor strings compliant with the HGVS standard</description>
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
iuc
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4 <macros>
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iuc
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5 <token name="@VERSION@">0.1.0</token>
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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6 <token name="@GALAXY_VERSION@">0</token>
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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7 </macros>
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
iuc
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8 <requirements>
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9 <requirement type="package" version="4.0">r-base</requirement>
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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10 </requirements>
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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11 <required_files>
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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12 <include path="parseHGVS.R" />
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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13 <include path="buildHGVS.R" />
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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14 </required_files>
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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15 <command detect_errors="exit_code"><![CDATA[
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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16 Rscript '$configscript' > tmp_output.csv
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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17 ]]>
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18 </command>
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19 <configfiles>
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20 <configfile name="configscript"><![CDATA[
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21 input_file <- '$action_choice.input_file'
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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22 input_data <- read.csv(input_file, stringsAsFactors = FALSE)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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23 #if $action_choice.do == "parse":
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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24 source('$__tool_directory__/parseHGVS.R')
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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25 #if $variant_format == "vcf":
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26 values <- paste0("p.", input_data$'$pos_col')
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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27 #else:
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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28 values <- input_data$'$pos_col'
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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29 #end if
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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30 out_data <- parseHGVS(values)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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31 result <- data.frame(
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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32 hgvs = out_data$'hgvs',
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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33 subject = out_data$'subject',
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34 type = out_data$'type',
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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35 start = out_data$'start',
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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36 ancestral = out_data$'ancestral',
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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37 variant = out_data$'variant'
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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38 )
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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39 #else if $action_choice.do == "build":
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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40 source('$__tool_directory__/buildHGVS.R')
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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41 result <- data.frame()
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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42 for (i in 1:nrow(input_data)) {
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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43 startPos <- input_data$'$startPos'[i]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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44 startAA <- input_data$'$startAA'[i]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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45 endAA <- input_data$'$endAA'[i]
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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46 #if $variant_format == "vcf":
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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47 builder <- new.hgvs.builder.p(1)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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48 result_build <- sub("^p\\.", "", with(builder, substitution(startPos, startAA, endAA)))
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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49 #else if $variant_format == "classic":
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50 builder <- new.hgvs.builder.p(1)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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51 result_build <- with(builder, substitution(startPos, startAA, endAA))
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52 #else:
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53 builder <- new.hgvs.builder.p(3)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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54 result_build <- with(builder, substitution(startPos, startAA, endAA))
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55 #end if
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56 result_row <- cbind(input_data[i, ], result_build)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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57 result <- rbind(result, result_row)
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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58 }
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59 #end if
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60 write.csv(result, file = "tmp_output.csv", row.names = FALSE, na="")
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61 ]]>
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62 </configfile>
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63 </configfiles>
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64 <inputs>
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65 <conditional name="action_choice">
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66 <param name="do" type="select" label="Choose the action" >
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67 <option value="parse" selected="true">parse</option>
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68 <option value="build">build</option>
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69 </param>
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70 <when value="parse" >
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71 <param name="input_file" type="data" format="csv" label="Input file" help="File containing column with variant descriptor strings" />
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72 <param name="pos_col" type="select" label="Variant descriptor column" help="The name of the column in the file that contains the variant descriptor, e.g. p.Glu214aAla (HGVS notation), p.A435D (classic notation), A435D (amino acid change descriptor format used in VCF)">
c12a4d187121 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hgvsparser/ commit f9deb29cdbd2d2a5f2f4fbd470b1078431a36ae0
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73 <options>
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74 <filter type="data_meta" ref="input_file" key="column_names"/>
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75 </options>
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76 </param>
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77 </when>
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78 <when value="build">
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79 <param name="input_file" type="data" format="csv" label="Input file" help="File containing columns with mutation position, ancestral amino acid, and variant amino acid" />
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80 <param name="startPos" type="select" label="Mutation position">
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81 <options>
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82 <filter type="data_meta" ref="input_file" key="column_names"/>
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83 </options>
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84 </param>
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85 <param name="startAA" type="select" label="Ancestral amino acid">
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86 <options>
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87 <filter type="data_meta" ref="input_file" key="column_names"/>
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88 </options>
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89 </param>
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90 <param name="endAA" type="select" label="Variant amino acid">
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91 <options>
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92 <filter type="data_meta" ref="input_file" key="column_names"/>
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93 </options>
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94 </param>
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95 </when>
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96 </conditional>
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97 <param name="variant_format" type="select" label="Variant descriptor format" help="For parsing: choose the format to parse. For building: choose the desired format for the result, regardless of the input format.">
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98 <option value="hgvs" selected="true">HGVS (e.g., p.Glu214aAla)</option>
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99 <option value="classic">classic (e.g., p.A435D)</option>
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100 <option value="vcf">Amino Acid Change used in VCF (e.g., A435D)</option>
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101 </param>
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102 </inputs>
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103 <outputs>
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104 <data name="outfile_parsed" format="csv" from_work_dir="tmp_output.csv" label="parseHGVS result on ${on_string}">
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105 <filter>action_choice['do'] == 'parse'</filter>
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106 </data>
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107 <data name="outfile_built" format="csv" from_work_dir="tmp_output.csv" label="buildHGVS result on ${on_string}">
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108 <filter>action_choice['do'] == 'build'</filter>
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109 </data>
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110 </outputs>
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111 <tests>
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112 <test expect_num_outputs="1">
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113 <!--test 1: parse-->
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114 <param name="variant_format" value="hgvs"/>
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115 <conditional name="action_choice">
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116 <param name="do" value="parse"/>
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117 <param name="input_file" value="inputParser.csv"/>
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118 <param name="pos_col" value="hgvs_pro"/>
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119 </conditional>
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120 <output name="outfile_parsed" ftype="csv">
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121 <assert_contents>
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122 <has_text text="ancestral"/>
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123 </assert_contents>
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124 </output>
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125 </test>
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126 <test expect_num_outputs="1">
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127 <!--test 2: build-->
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128 <param name="variant_format" value="hgvs"/>
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129 <conditional name="action_choice">
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130 <param name="do" value="build"/>
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131 <param name="input_file" value="inputBuilder.csv"/>
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132 <param name="startPos" value="start"/>
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133 <param name="startAA" value="ancestral"/>
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134 <param name="endAA" value="variant"/>
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135 </conditional>
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136 <output name="outfile_built" ftype="csv">
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137 <assert_contents>
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138 <has_text text="build"/>
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139 </assert_contents>
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140 </output>
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141 </test>
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142 </tests>
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143 <help><![CDATA[
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144 **What it does**
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145
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146 This tool parses and builds variant descriptor strings compliant with the HGVS standard.
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147
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148 ]]></help>
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149 <citations>
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150 <citation type="doi">10.1186/s13059-019-1845-6</citation>
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151 </citations>
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152 </tool>