--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seq2HLA.xml	Thu Dec 20 10:37:01 2012 -0500
@@ -0,0 +1,79 @@
+<tool id="seqhla" name="seq2HLA" version="1.0.0">
+    <description>HLA typing from RNA-Seq sequence read</description>
+    <command interpreter="python">
+      seq2HLA.py
+      -z $compressed
+      -1 $readFile1
+      -2 $readFile2
+      -r $runName
+      -l $readLength
+      -3 $trim
+      -o $out1
+      -p $out2
+      -g $logfile
+    </command>
+    <inputs>
+      <param name="compressed" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Select if your input files are compressed gzipped fastq files" help="Leave default if you didn't upload the files or don't know"/>
+      <param format="fastq,fastqsanger" name="readFile1" type="data" label="Forward FASTQ File" help="FASTQ File with forward reads" />
+      <param format="fastq,fastqsanger" name="readFile2" type="data" label="Reverse FASTQ File" help="FASTQ File with reverse reads" />
+      <param name="runName" type="text" value="Run1" label="Run Name" help="Name of the Run" />
+      <param name="readLength" type="integer" value="50" label="Read Length" help="Length of the input reads" />
+      <param name="trim" type="integer" value="0" label="Trim x bases from the low quality 3' end" help="Trim x bases from the low quality 3' end. Default: 0" />
+    </inputs>
+    <outputs>
+      <data format="txt" name="out1" label="${tool.name} on ${on_string}: Output 1" />
+      <data format="txt" name="out2" label="${tool.name} on ${on_string}: Output 2" />
+      <data format="txt" name="logfile" label="${tool.name} on ${on_string}: Log" />
+    </outputs>
+    <tests>
+      <test>
+	<param name="compressed" value="True"/>
+	<param name="readFile1" ftype="fastq" value="input1.fq"/>
+	<param name="readFile2" ftype="fastq" value="input2.fq"/>
+	<param name="runName" value="Run1"/>
+	<param name="readLength" value="37"/>
+	<param name="trim" value="0"/>
+	<output name="out1" file="output1.txt"/>
+	<output name="out2" file="output2.txt"/>
+	<output name="logfile" file="log.txt"/>
+      </test>
+    </tests>
+<help>
+.. class:: infomark
+
+**What it does**
+
+We developed an in-silico method "seq2HLA", written in python and R, which takes standard paired end RNA-Seq sequence reads in fastq format
+as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes, a p-value for each call, and the expression of each class.
+
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+Input files in FASTQ format
+
+-----
+
+.. class:: infomark
+
+**Output**
+
+Output file(s) in TXT format
+
+-----
+
+.. class:: infomark
+
+**Authors**
+
+Sebastian Boegel
+
+-----
+
+.. image:: ./static/images/tron_logo.png
+
+</help>
+</tool>