--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ecoli_serotyping/ectyper.xml	Fri Jan 05 09:17:33 2018 -0500
@@ -0,0 +1,80 @@
+<tool id="ectyper" name="ectyper" version="2.0">
+    <requirements>
+      <requirement type="package" version="3.6.3">python</requirement>
+      <requirement type="package">biopython</requirement>
+      <requirement type="package">blast</requirement>
+      <requirement type="package">samtools</requirement>
+      <requirement type="package">bcftools</requirement>
+      <requirement type="package">bowtie</requirement>
+      <requirement type="package">spades</requirement>
+      <requirement type="package">seqtk</requirement>
+#      <requirement type="package">mash</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+     
+      ln -s $fasta1 sample_1.fastq;  
+      ln -s $fastq2 sample_2.fastq;  
+
+      $__tool_directory__/ectyper.py
+      -i ecoliA.fasta for a single file
+      -i ecoliA.fasta,ecoliB.fastq,ecoliC.fna for multiple files
+      -i ecoli_folder for a folder
+      -i ecoli_folder for a folder
+      -d PERCENTIDENTITY
+      -l PERCENTLENGTH
+      -o OUTPUT; 
+      cat  SeqSero_result*/Seqsero_result.txt > results.txt; 
+
+    ]]></command>
+    <inputs>
+          <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
+          <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" />
+          <param name="numofthr" type="select" label="Number of threads">
+          <option value="1">1</option>
+          <option value="2">2</option>
+          <option value="3">3</option>
+          <option value="4">4</option>
+        </param>
+        <param name="maptype" type="select" label="Algorithms for BWA mapping?">
+          <option value="mem">mem</option>
+          <option value="sam">sam</option>
+        </param>
+    
+
+    </inputs>
+    <outputs>
+      <data format="txt" label="ectyper Results" name="results" from_work_dir="results.txt"/>
+    </outputs>
+    <tests>
+       <test>
+         <output name="results" file="results.txt"/>
+       </test>
+    </tests>
+    <help><![CDATA[
+    
+**Usage: ectyper**
+
+**INPUT**
+
+Location of new file(s). Can be a single file or a directory
+
+**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%.
+
+**verify**
+
+Enable E. Coli. verification
+
+**species**
+
+Enable species identification when non-ecoli genome is found Note: refseq downloading is required when running this option for the first time.
+
+**OUTPUT**
+Directory location of output files.
+    ]]></help>
+</tool>