--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/ilmn_pacbio/soap_denovo.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,73 @@
+<tool id="soap_denovo" name="SOAPdenovo" version="1.0.0">
+  <description>Short-read de novo assembly</description>
+  <!--
+      # SOAPdenovo-127mer all -s ${soap_config} -o assembly -K ${k} -p 8 -d -D
+      # cat ${soap_config} > ${output1}
+      # cp ${soap_config} ${output1} &amp;&amp;
+  -->
+  <command>
+      SOAPdenovo-127mer all -s ${soap_config} -o assembly -K ${k} -p 24 -d -D -R
+  </command>
+  <inputs>
+    <conditional name="inputs">
+      <param name="read_type" type="select" label="Illumina read type">
+        <option value="single">Single fragment</option>
+        <option value="paired">Paired-end</option>
+      </param>
+      <when value="single">
+        <param name="input1" format="fastq" type="data" label="FASTQ file for reads"/>
+      </when>
+      <when value="paired">
+        <param name="input1" format="fastq" type="data" label="FASTQ file for forward reads"/>
+        <param name="input2" format="fastq" type="data" label="FASTQ file for reverse reads"/>
+        <param name="d" type="integer" value="500" label="Estimated insert size for paired-end reads" />
+      </when>
+    </conditional>
+    <param name="k" type="integer" value="23" label="Size of k for forming the de Bruijn overlap graph" />
+  </inputs>
+  <configfiles>
+    <configfile name="soap_config">max_rd_len=105
+[LIB]
+#if $inputs.read_type == "single"
+q=${inputs.input1.file_name}
+#else
+avg_ins=${inputs.d}
+asm_flags=3
+reverse_seq=0
+q1=${inputs.input1.file_name}
+q2=${inputs.input2.file_name}
+#end if
+    </configfile>
+  </configfiles>
+  <outputs>
+    <data name="assembled_contigs" format="fasta" from_work_dir="assembly.scafSeq" label="Assembled contigs from ${on_string}" />
+  </outputs>
+  <help>
+
+**What it does**
+
+Runs SOAPdenovo_ to generate a genome assembly
+using single-fragment or paired-end short reads.
+
+Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J.
+"De novo assembly of human genomes with massively parallel short read sequencing."
+*Genome Res.* 2010 Feb;20(2):265-72.
+
+.. _SOAPdenovo: http://soap.genomics.org.cn/soapdenovo.html
+
+**Parameter list**
+
+k
+    k-mer size for constructing the de Bruijn graph.  The appropriate size of k is genome and data set dependent, but a good starting choice might be 75% of the read length.
+
+Insert size
+    For paired-end libraries, the expected insert size.
+
+**Output**
+
+assembly
+
+  </help>
+</tool>
+
+