# HG changeset patch
# User jpetteng
# Date 1515515767 18000
# Node ID 3853eaea6e00c0d7736fd429b7e5423eb8c001fd
# Parent  cad63e627e0a51a22e46f545b3b9e2138149bd57
Uploaded

diff -r cad63e627e0a -r 3853eaea6e00 ecoli_serotyping/ectyper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ecoli_serotyping/ectyper.xml	Tue Jan 09 11:36:07 2018 -0500
@@ -0,0 +1,103 @@
+<tool id="ectyper" name="ectyper" version="2.0">
+    <requirements>
+      <requirement type="package" version="3.6.3">python</requirement>
+      <requirement type="package">ectyper</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">pandas</requirement>
+      <requirement type="package">mash</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+      #if $jobtype.select == "asm"
+        ln -s $jobtype.draft sample.fasta;  
+      #else if $jobtype.select == "se"
+        ln -s $jobtype.fastq1 sample_1.fastq;  
+      #else if $jobtype.select == "pe"
+        ln -s $jobtype.fastq1 sample_1.fastq;  
+        ln -s $jobtype.fastq2 sample_2.fastq;  
+      #end if
+
+      python $__tool_directory__/bin/ectyper
+      #if $jobtype.select == "asm"
+        -m 4
+        -i sample.fasta
+      #else if $jobtype.select == "se"
+        -m 3
+        -i sample_1.fastq
+      #else if $jobtype.select == "pe"
+        -m 2
+        -i sample_1.fastq sample_2.fastq
+      #end if
+      -b $maptype.select;
+      cat  ectyper_result*/ectyper_result.txt > results.txt; 
+
+    ]]></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>
+        </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>
+      </conditional>
+
+      <conditional name="maptype">
+        <param name="select" type="select" label="Algorithms for BWA mapping?">
+          <option value="sam">sam</option>
+          <option value="mem">mem</option>
+        </param>
+      </conditional>
+    
+
+    </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**
+
+A fasta assembly
+
+**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>