Mercurial > repos > nml > mykrobe_parser

changeset 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
files mykrobe_parser.xml
diffstat 1 files changed, 16 insertions(+), 37 deletions(-) [+]
line wrap: on
line diff
--- a/mykrobe_parser.xml	Tue Oct 23 08:54:51 2018 -0400
+++ b/mykrobe_parser.xml	Fri Oct 26 16:57:34 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="mykrobe_parseR" name="mykrobe_parseR" version="0.1.2">
+<tool id="mykrobe_parseR" name="mykrobe_parseR" version="0.1.3">
     <requirements>
         <requirement type="package" version="3.4.1">r-base</requirement>
         <requirement type="package" version="1.5.0">r-jsonlite</requirement>
@@ -10,21 +10,16 @@
 	<requirement type="package" version="1.3.0">r-stringr</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        
-        #if $input.type == 'collection'
-            mkdir collection_files &&
-            #for $file in $input.collection
-                ln -s "$file" collection_files/"$file.element_identifier".json &&
-            #end for
-        #end if
+
+	mkdir collection_files &&
+
+        #for $file in $input
+            ln -s "$file" collection_files/"$file.element_identifier".json &&
+        #end for
 
         Rscript "$__tool_directory__/mykrobe_parser.R"
 
-        #if $input.type =='single'
-            -f "$input.single"
-        #else
-            -d "collection_files"
-        #end if
+        -d "collection_files"
 
         #if $version
             -v "$version"
@@ -41,26 +36,11 @@
 
     ]]></command>
     <inputs>
-    <conditional name="input">
-      <param name="type" type="select" label="Sequence Data Type">
-        <option value="single">Single JSON File</option>
-        <option value="collection">Collection of JSON Files</option>
-      </param>
-      <when value="single">
-        <param name="single"
-          type="data" format="json,txt"
-          optional="false"
-          label="Single JSON File (.JSON or .TXT)"
-          />
-      </when>
-      <when value="collection">
-        <param name="collection"
-          type="data_collection" format="json,txt"
-          optional="false"
-          label="Collection of JSON Files (.JSON or .TXT)"
-          />
-      </when>
-    </conditional>
+    <param name="input"
+        type="data" format="json,txt"
+        optional="false"
+        multiple="true"
+        label="JSON File(s) (.JSON or .TXT)"/>
     <param name="version" type="text"
         argument="-v"
         optional="true"
@@ -86,10 +66,9 @@
     </outputs>
     <tests>
         <test>
-            <param name="type" value="single"/>
-            <param name="single" ftype="json" value="test-data.json"/>
-            <output name="output-jsondata" ftype="csv" value="output-jsondata.csv" compare="sim_size"/>
-            <output name="output-report" ftype="csv" value="output-report.csv" compare="sim_size"/>
+		<param name="input" value="test-data.json"/>
+		<output name="output-jsondata" ftype="csv" value="output-jsondata.csv" compare="sim_size"/>
+        	<output name="output-report" ftype="csv" value="output-report.csv" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[