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comparison mykrobe_parser.xml @ 3:0dcfdec76c3c draft

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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 44e99120db3fc06ca9302bc52687b00424e8b478
author nml
date Fri, 26 Oct 2018 16:57:34 -0400
parents f2608dccd3e0
children 8529045f0fdf
comparison
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2:f2608dccd3e0 3:0dcfdec76c3c
1 <tool id="mykrobe_parseR" name="mykrobe_parseR" version="0.1.2"> 1 <tool id="mykrobe_parseR" name="mykrobe_parseR" version="0.1.3">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="3.4.1">r-base</requirement> 3 <requirement type="package" version="3.4.1">r-base</requirement>
4 <requirement type="package" version="1.5.0">r-jsonlite</requirement> 4 <requirement type="package" version="1.5.0">r-jsonlite</requirement>
5 <requirement type="package" version="0.1.0">r-here</requirement> 5 <requirement type="package" version="0.1.0">r-here</requirement>
6 <requirement type="package" version="0.7.6">r-dplyr</requirement> 6 <requirement type="package" version="0.7.6">r-dplyr</requirement>
8 <requirement type="package" version="0.8.1">r-tidyr</requirement> 8 <requirement type="package" version="0.8.1">r-tidyr</requirement>
9 <requirement type="package" version="1.6.0">r-optparse</requirement> 9 <requirement type="package" version="1.6.0">r-optparse</requirement>
10 <requirement type="package" version="1.3.0">r-stringr</requirement> 10 <requirement type="package" version="1.3.0">r-stringr</requirement>
11 </requirements> 11 </requirements>
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 13
14 #if $input.type == 'collection' 14 mkdir collection_files &&
15 mkdir collection_files && 15
16 #for $file in $input.collection 16 #for $file in $input
17 ln -s "$file" collection_files/"$file.element_identifier".json && 17 ln -s "$file" collection_files/"$file.element_identifier".json &&
18 #end for 18 #end for
19 #end if
20 19
21 Rscript "$__tool_directory__/mykrobe_parser.R" 20 Rscript "$__tool_directory__/mykrobe_parser.R"
22 21
23 #if $input.type =='single' 22 -d "collection_files"
24 -f "$input.single"
25 #else
26 -d "collection_files"
27 #end if
28 23
29 #if $version 24 #if $version
30 -v "$version" 25 -v "$version"
31 #end if 26 #end if
32 #if $depth 27 #if $depth
39 -n "$run_name" 34 -n "$run_name"
40 #end if 35 #end if
41 36
42 ]]></command> 37 ]]></command>
43 <inputs> 38 <inputs>
44 <conditional name="input"> 39 <param name="input"
45 <param name="type" type="select" label="Sequence Data Type"> 40 type="data" format="json,txt"
46 <option value="single">Single JSON File</option> 41 optional="false"
47 <option value="collection">Collection of JSON Files</option> 42 multiple="true"
48 </param> 43 label="JSON File(s) (.JSON or .TXT)"/>
49 <when value="single">
50 <param name="single"
51 type="data" format="json,txt"
52 optional="false"
53 label="Single JSON File (.JSON or .TXT)"
54 />
55 </when>
56 <when value="collection">
57 <param name="collection"
58 type="data_collection" format="json,txt"
59 optional="false"
60 label="Collection of JSON Files (.JSON or .TXT)"
61 />
62 </when>
63 </conditional>
64 <param name="version" type="text" 44 <param name="version" type="text"
65 argument="-v" 45 argument="-v"
66 optional="true" 46 optional="true"
67 label="Mykrobe Workflow Version"/> 47 label="Mykrobe Workflow Version"/>
68 <param name="depth" type="integer" 48 <param name="depth" type="integer"
84 <data name="output-jsondata" from_work_dir="output-jsondata.csv" format="csv" label="jsondata"/> 64 <data name="output-jsondata" from_work_dir="output-jsondata.csv" format="csv" label="jsondata"/>
85 <data name="output-report" from_work_dir="output-report.csv" format="csv" label="report"/> 65 <data name="output-report" from_work_dir="output-report.csv" format="csv" label="report"/>
86 </outputs> 66 </outputs>
87 <tests> 67 <tests>
88 <test> 68 <test>
89 <param name="type" value="single"/> 69 <param name="input" value="test-data.json"/>
90 <param name="single" ftype="json" value="test-data.json"/> 70 <output name="output-jsondata" ftype="csv" value="output-jsondata.csv" compare="sim_size"/>
91 <output name="output-jsondata" ftype="csv" value="output-jsondata.csv" compare="sim_size"/> 71 <output name="output-report" ftype="csv" value="output-report.csv" compare="sim_size"/>
92 <output name="output-report" ftype="csv" value="output-report.csv" compare="sim_size"/>
93 </test> 72 </test>
94 </tests> 73 </tests>
95 <help><![CDATA[ 74 <help><![CDATA[
96 ============== 75 ==============
97 Mykrobe Parser 76 Mykrobe Parser