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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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-1:000000000000 0:c12a4d187121
1 <tool id="hgvsparser" name="hgvsParseR" version="@VERSION@+galaxy@GALAXY_VERSION@" profile="20.09"
2 license="GPL-3.0" >
3 <description>parsing and building variant descriptor strings compliant with the HGVS standard</description>
4 <macros>
5 <token name="@VERSION@">0.1.0</token>
6 <token name="@GALAXY_VERSION@">0</token>
7 </macros>
8 <requirements>
9 <requirement type="package" version="4.0">r-base</requirement>
10 </requirements>
11 <required_files>
12 <include path="parseHGVS.R" />
13 <include path="buildHGVS.R" />
14 </required_files>
15 <command detect_errors="exit_code"><![CDATA[
16 Rscript '$configscript' > tmp_output.csv
17 ]]>
18 </command>
19 <configfiles>
20 <configfile name="configscript"><![CDATA[
21 input_file <- '$action_choice.input_file'
22 input_data <- read.csv(input_file, stringsAsFactors = FALSE)
23 #if $action_choice.do == "parse":
24 source('$__tool_directory__/parseHGVS.R')
25 #if $variant_format == "vcf":
26 values <- paste0("p.", input_data$'$pos_col')
27 #else:
28 values <- input_data$'$pos_col'
29 #end if
30 out_data <- parseHGVS(values)
31 result <- data.frame(
32 hgvs = out_data$'hgvs',
33 subject = out_data$'subject',
34 type = out_data$'type',
35 start = out_data$'start',
36 ancestral = out_data$'ancestral',
37 variant = out_data$'variant'
38 )
39 #else if $action_choice.do == "build":
40 source('$__tool_directory__/buildHGVS.R')
41 result <- data.frame()
42 for (i in 1:nrow(input_data)) {
43 startPos <- input_data$'$startPos'[i]
44 startAA <- input_data$'$startAA'[i]
45 endAA <- input_data$'$endAA'[i]
46 #if $variant_format == "vcf":
47 builder <- new.hgvs.builder.p(1)
48 result_build <- sub("^p\\.", "", with(builder, substitution(startPos, startAA, endAA)))
49 #else if $variant_format == "classic":
50 builder <- new.hgvs.builder.p(1)
51 result_build <- with(builder, substitution(startPos, startAA, endAA))
52 #else:
53 builder <- new.hgvs.builder.p(3)
54 result_build <- with(builder, substitution(startPos, startAA, endAA))
55 #end if
56 result_row <- cbind(input_data[i, ], result_build)
57 result <- rbind(result, result_row)
58 }
59 #end if
60 write.csv(result, file = "tmp_output.csv", row.names = FALSE, na="")
61 ]]>
62 </configfile>
63 </configfiles>
64 <inputs>
65 <conditional name="action_choice">
66 <param name="do" type="select" label="Choose the action" >
67 <option value="parse" selected="true">parse</option>
68 <option value="build">build</option>
69 </param>
70 <when value="parse" >
71 <param name="input_file" type="data" format="csv" label="Input file" help="File containing column with variant descriptor strings" />
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)">
73 <options>
74 <filter type="data_meta" ref="input_file" key="column_names"/>
75 </options>
76 </param>
77 </when>
78 <when value="build">
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" />
80 <param name="startPos" type="select" label="Mutation position">
81 <options>
82 <filter type="data_meta" ref="input_file" key="column_names"/>
83 </options>
84 </param>
85 <param name="startAA" type="select" label="Ancestral amino acid">
86 <options>
87 <filter type="data_meta" ref="input_file" key="column_names"/>
88 </options>
89 </param>
90 <param name="endAA" type="select" label="Variant amino acid">
91 <options>
92 <filter type="data_meta" ref="input_file" key="column_names"/>
93 </options>
94 </param>
95 </when>
96 </conditional>
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.">
98 <option value="hgvs" selected="true">HGVS (e.g., p.Glu214aAla)</option>
99 <option value="classic">classic (e.g., p.A435D)</option>
100 <option value="vcf">Amino Acid Change used in VCF (e.g., A435D)</option>
101 </param>
102 </inputs>
103 <outputs>
104 <data name="outfile_parsed" format="csv" from_work_dir="tmp_output.csv" label="parseHGVS result on ${on_string}">
105 <filter>action_choice['do'] == 'parse'</filter>
106 </data>
107 <data name="outfile_built" format="csv" from_work_dir="tmp_output.csv" label="buildHGVS result on ${on_string}">
108 <filter>action_choice['do'] == 'build'</filter>
109 </data>
110 </outputs>
111 <tests>
112 <test expect_num_outputs="1">
113 <!--test 1: parse-->
114 <param name="variant_format" value="hgvs"/>
115 <conditional name="action_choice">
116 <param name="do" value="parse"/>
117 <param name="input_file" value="inputParser.csv"/>
118 <param name="pos_col" value="hgvs_pro"/>
119 </conditional>
120 <output name="outfile_parsed" ftype="csv">
121 <assert_contents>
122 <has_text text="ancestral"/>
123 </assert_contents>
124 </output>
125 </test>
126 <test expect_num_outputs="1">
127 <!--test 2: build-->
128 <param name="variant_format" value="hgvs"/>
129 <conditional name="action_choice">
130 <param name="do" value="build"/>
131 <param name="input_file" value="inputBuilder.csv"/>
132 <param name="startPos" value="start"/>
133 <param name="startAA" value="ancestral"/>
134 <param name="endAA" value="variant"/>
135 </conditional>
136 <output name="outfile_built" ftype="csv">
137 <assert_contents>
138 <has_text text="build"/>
139 </assert_contents>
140 </output>
141 </test>
142 </tests>
143 <help><![CDATA[
144 **What it does**
145
146 This tool parses and builds variant descriptor strings compliant with the HGVS standard.
147
148 ]]></help>
149 <citations>
150 <citation type="doi">10.1186/s13059-019-1845-6</citation>
151 </citations>
152 </tool>