--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/skesa.xml	Mon Aug 13 17:17:00 2018 -0400
@@ -0,0 +1,77 @@
+<tool id="skesa" name="skesa" version="0.1">
+    <requirements>
+      <requirement type="package" version="0.1">skesa</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    #if $jobtype.select != "cl"
+	skesa
+      #if $jobtype.select == "asm"
+        -i ${draft.name}.fasta
+      #else if $jobtype.select == "se"
+        --fastq ${fastq1.name}.fastq
+      #else if $jobtype.select == "pe"
+	--fastq ${fastq1.name}.fastq,${fastq2.name}.fastq
+      #end if
+	--use_paired_ends > results.skesa.fasta
+    #end if 
+
+    ]]></command>
+    <inputs>
+      <conditional name="jobtype">
+        <param name="select" type="select" label="Assembly or FASTQ Reads?">
+          <option value="asm">Genome Assembly</option>
+          <option value="se">Single-End Reads</option>
+          <option value="pe">Paired-End Reads</option>
+          <option value="cl">Collection of Reads</option>
+        </param>
+        <when value="asm">
+          <param name="draft" type="data" format="fasta" label="FASTA" />
+        </when>
+        <when value="se">
+          <param name="fastq1" type="data" format="fastq" label="FASTQ" />
+        </when>
+        <when value="pe">
+          <param name="fastq1" type="data" format="fastq" label="FASTQ" />
+          <param name="fastq2" type="data" format="fastq" label="FASTQ" />
+        </when>
+         <when value="cl">
+              <param type="data_collection" name="collection_files" format="fastq" collection_type="list" label="FASTQS:  Must be a Data Set list built from multiple fastq files" />
+        </when>
+      </conditional>
+   
+      <param name="percent_identity" type="integer" label="Percent identity required for an allele match [default 90]" value="90" />
+      <param name="percent_length" type="integer" label="Percent length required for an allele match [default 50]" value="50" />
+    
+    </inputs>
+    <outputs>
+            <data format="fasta" label="skesa Results" name="${input.name}.skesa.fasta" from_work_dir="*.fasta"/>
+    </outputs>
+
+    <help><![CDATA[
+    
+**Usage: skesa**
+
+**INPUT**
+
+A fasta assembly or single or paired end reads test or data set list of fastqs
+
+**PERCENTIDENTITY**
+
+Percentage of identity wanted to use against the database. From 0 to 100, default is 90%.
+
+**PERCENTLENGTH**
+
+Percentage of length wanted to use against the database. From 0 to 100, default is 50%.
+
+https://github.com/phac-nml/ecoli_serotyping
+
+    ]]></help>
+     <citations>
+        <citation type="bibtex">
+        @misc{pope_dashnow_zobel_holt_raven_schultz_inouye_tomita_2014,
+        title={SRST2: ecyper wraps a standalone serotyping module for Escherichia coli. Supports fasta and fastq file formats.},
+        url={https://www.nml-lnm.gc.ca/},
+        author={National Microbiology Laboratory },
+       }</citation>
+    </citations>
+</tool>