diff mykrobe_parser.xml @ 0:6eae14751768 draft

planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 0b64469b5d819a9c5b9ea85d07ccbc3b5fb6b25e-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mykrobe_parser.xml	Fri Sep 28 16:01:47 2018 -0400
@@ -0,0 +1,136 @@
+<tool id="mykrobe_parseR" name="mykrobe_parseR" version="0.1.0">
+    <requirements>
+        <requirement type="package" version="3.4.1">r-base</requirement>
+        <requirement type="package" version="1.5.0">r-jsonlite</requirement>
+        <requirement type="package" version="0.1.0">r-here</requirement>
+        <requirement type="package" version="0.7.6">r-dplyr</requirement>
+        <requirement type="package" version="0.2.5">r-purrr</requirement>
+        <requirement type="package" version="0.8.1">r-tidyr</requirement>
+        <requirement type="package" version="1.6.0">r-optparse</requirement>
+	<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 $input.collection
+                cp "$file" collection_files/"$file.name".json &&
+            #end for
+        #end if
+
+        Rscript "$__tool_directory__/mykrobe_parser.R"
+
+        #if $input.type =='single'
+            -f "$input.single"
+        #else
+            -d "collection_files"
+        #end if
+
+        #if $version
+            -v "$version"
+        #end if
+        #if $depth
+            -D "$depth"
+        #end if
+        #if $confidence
+            -c "$confidence"
+        #end if
+        #if $run_name
+            -n "$run_name"
+        #end if
+
+    ]]></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="version" type="text"
+        argument="-v"
+        optional="true"
+        label="Mykrobe Workflow Version"/>
+    <param name="depth" type="integer"
+        argument="-D"
+        optional="true"
+        label="Minimum depth of coverage"
+        help="Enter integer values only. Default is 5"/>
+    <param name="confidence" type="integer"
+        argument="-c"
+        optional="true"
+        label="Confidence"
+        help="Minimum genotype confidence for variant genotyping. Enter integer values only. Default is 10"/>
+    <param name="run_name" type="text"
+        argument="-n"
+        optional="true"
+        label="Name of Run"/>
+    </inputs>
+    <outputs>
+        <data name="output-jsondata" from_work_dir="output-jsondata.csv" format="csv" label="jsondata"/>
+        <data name="output-report" from_work_dir="output-report.csv" format="csv" label="report"/>
+    </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"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+==============
+Mykrobe Parser
+==============
+
+R Script to parse the results of mykrobe predictor and present them in a LIMS compatible format.
+
+=====
+Legal 
+=====
+
+Copyright Government of Canada 2018
+
+Written by: National Microbiology Laboratory, Public Health Agency of Canada
+
+Licensed under the Apache License, Version 2.0 (the "License"); you may not use
+this work except in compliance with the License. You may obtain a copy of the
+License at:
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software distributed
+under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
+CONDITIONS OF ANY KIND, either express or implied. See the License for the
+specific language governing permissions and limitations under the License.
+
+=======
+Contact
+=======
+
+**Gary van Domselaar**: [e-mail]
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">@ARTICLE{a1,
+            title = {R Script to parse the results of mykrobe predictor and present them in a LIMS compatible format.},
+            author = {Adrian Zetner},
+            url = {https://github.com/phac-nml/mykrobe-parser}
+            }
+        }</citation>
+    </citations>
+</tool>