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comparison mykrobe_parser.xml @ 1:05ca0dbc9f46 draft

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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 2d42861c536b44c4fe00bef20c442c6cc0e987dd-dirty
author nml
date Mon, 01 Oct 2018 14:54:34 -0400
parents 6eae14751768
children f2608dccd3e0
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0:6eae14751768 1:05ca0dbc9f46
1 <tool id="mykrobe_parseR" name="mykrobe_parseR" version="0.1.0"> 1 <tool id="mykrobe_parseR" name="mykrobe_parseR" version="0.1.1">
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>
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 13
14 #if $input.type == 'collection' 14 #if $input.type == 'collection'
15 mkdir collection_files && 15 mkdir collection_files &&
16 #for $file in $input.collection 16 #for $file in $input.collection
17 cp "$file" collection_files/"$file.name".json && 17 ln -s "$file" collection_files/"$file.element_identifier".json &&
18 #end for 18 #end for
19 #end if 19 #end if
20 20
21 Rscript "$__tool_directory__/mykrobe_parser.R" 21 Rscript "$__tool_directory__/mykrobe_parser.R"
22 22