# HG changeset patch
# User jowong
# Date 1541381773 18000
# Node ID 376f0194b92ab6f5080441016e65d8cc9489bb05

planemo upload

diff -r 000000000000 -r 376f0194b92a spotyping.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spotyping.xml	Sun Nov 04 20:36:13 2018 -0500
@@ -0,0 +1,47 @@
+<tool id="spotyping" name="Spoligotype Prediction" version="0.1.0">
+    <requirements>
+        <requirement type="package" version="2.1">spotyping</requirement>
+    </requirements>
+    <command>
+        python SpoTyping.py 
+        #if str( $data_input.data_selector ) == "paired"       
+            $data_input.input1.forward $data_input.input1.reverse
+        #end if
+        #if str( $data_input.data_selector ) == "single"       
+            $data_input.input2.element_identifier
+        #end if
+    ></command>
+    <inputs>
+        <conditional name="data_input">
+          <param name="data_selector" type="select" label="Single or Paired-end Data" help="Select between paired and single end data to add name to dataset">
+            <option value="paired">Paired</option>
+            <option value="single">Single</option>
+          </param>
+          <when value="paired">
+            <param name="input1" format="data" type="data_collection" collection_type="paired" label="Select a paired collection" help="a paired data"/>
+          </when>
+          <when value="single">
+            <param name="input2" format="data" type="data" label="input" help="Specify dataset with single reads"/>
+          </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output1" label="spoligotyping results" format="data" from_work_dir="SpoTyping"/>
+        <data name="output2" label="spoligotyping log" format="data" from_work_dir="SpoTyping.log"/>
+        <data name="output3" label="query" format="data" from_work_dir="*.xls"/>
+    </outputs>
+    <help><![CDATA[
+        Usage: python SpoTyping.py [options] FASTQ_1/FASTA FASTQ_2(optional) 
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{githubSpoTyping,
+  author = {Xia, Eryu},
+  year = {2016},
+  title = {SpoTyping},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/xiaeryu/SpoTyping},
+}</citation>
+    </citations>
+</tool>