# HG changeset patch
# User jpetteng
# Date 1515612054 18000
# Node ID 4724d20b14debd7a7f77dbda259cadcb8ca0b45d

Uploaded

diff -r 000000000000 -r 4724d20b14de ectyper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ectyper.xml	Wed Jan 10 14:20:54 2018 -0500
@@ -0,0 +1,74 @@
+<tool id="ectyper" name="ectyper" version="0.1">
+    <requirements>
+      <requirement type="package" version="0.1">ectyper</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
+
+	  $__tool_directory__/ectyper 
+      #if $jobtype.select == "asm"
+        -i sample.fasta
+      #else if $jobtype.select == "se"
+        -i sample_1.fastq
+      #else if $jobtype.select == "pe"
+        -i sample_1.fastq sample_2.fastq
+      #end if
+      -d $percent_identity
+	  -l $percent_length
+  	  -o "./"; cat ./output/output.csv > results.csv; 
+
+    ]]></command>
+    <inputs>
+      <conditional name="jobtype">
+        <param name="select" type="select" label="Assembly or FASTQ Reads?">
+          <option value="asm">Genome Assembly</option>
+          <option value="se">Single-End Reads</option>
+          <option value="pe">Paired-End Reads</option>
+        </param>
+        <when value="asm">
+          <param name="draft" type="data" format="fasta" label="FASTA" />
+        </when>
+        <when value="se">
+          <param name="fastq1" type="data" format="fastq" label="FASTQ" />
+        </when>
+        <when value="pe">
+          <param name="fastq1" type="data" format="fastq" label="FASTQ" />
+          <param name="fastq2" type="data" format="fastq" label="FASTQ" />
+        </when>
+      </conditional>
+
+      <param name="percent_identity" type="integer" label="Percent identity required for an allele match [default 90]" value="90" />
+      <param name="percent_length" type="integer" label="Percent length required for an allele match [default 50]" value="50" />
+    
+    </inputs>
+    <outputs>
+            <data format="csv" label="ectyper Results" name="${input.name}.ectperResults" from_work_dir="*.csv"/>
+    </outputs>
+
+    <help><![CDATA[
+    
+**Usage: ectyper**
+
+**INPUT**
+
+A fasta assembly or single or paired end reads
+
+**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>
+</tool>