--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/novocraft_wrapper.xml	Wed Dec 17 10:13:11 2014 -0500
@@ -0,0 +1,188 @@
+<tool id="novocraft_wrapper" name="Novocraft" version="3.00.02">
+ <description>maps query reads onto the reference sequences</description>
+  <command interpreter="python">
+   novocraft_wrapper.py 
+   ## Parameters
+      --settings=$params.settingsType
+   #if $params.settingsType == "full":
+  	--align=${params.t}
+   	--open=${params.g}
+   	--extend=${params.x}
+   	--trunc=${params.n}
+   	--kmer=${params.k}
+   	--step=${params.s}
+   	--qual=${params.l}
+   	--repe=${params.m}
+   	--hclip=${params.H}
+   	--pam=$params.pairedEnd
+   	--sd=${params.d}
+   	--insert=${params.i}
+   #end if
+
+   #if $genomeSource.refGenomeSource == "history":
+        ##build index on the fly
+        --refer="${genomeSource.refFile}"
+        ##--dbkey=$dbkey
+      #else:
+        ##use precomputed indexes
+        --ref1="${genomeSource.indices.fields.path}"
+        ##--do_not_build_index
+   #end if
+
+   ## input file(s)
+      --input1=$paired.input1
+   #if $paired.sPaired == "paired":
+        --input2=$paired.input2
+   #end if
+
+   ## Outputs.
+   --output=$output
+
+</command>
+<inputs>
+    <conditional name="genomeSource">
+      <param name="refGenomeSource" type="select" label="Select a reference genome from your history or use a built-in index?">
+        <option value="indexed">Use a built-in index</option>
+        <option value="history">Use one from the history</option>
+      </param>
+
+      <when value="indexed">
+        <param name="indices" type="select" label="Select a reference genome">
+          <options from_data_table="novocraft_indexes">
+            <filter type="sort_by" column="2" />
+            <validator type="no_options" message="No indexes are available" />
+          </options>
+        </param>
+      </when>
+
+      <when value="history">
+        <param name="refFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
+      </when>
+    </conditional>
+
+    <conditional name="paired">
+      <param name="sPaired" type="select" label="Is this library mate-paired?">
+        <option value="single">Single-end</option>
+        <option value="paired">Paired-end</option>
+      </param>
+
+      <when value="single">
+        <param name="input1" type="data" format="fastq" label="FASTQ file" help="FASTQ with Sanger-scaled quality values (fastqsanger)" />
+      </when>
+      <when value="paired">
+        <param name="input1" type="data" format="fastq" label="Forward FASTQ file" help="FASTQ with Sanger-scaled quality values (fastqsanger)" />
+        <param name="input2" type="data" format="fastq" label="Reverse FASTQ file" help="FASTQ with Sanger-scaled quality values (fastqsanger)" />
+      </when>
+    </conditional>
+     <conditional name="params">
+            <param name="settingsType" type="select" label="Parameter Settings" help="You can use the default settings or set custom values for the parameters.">
+              <option value="preSet">Use Defaults</option>
+              <option value="full">Full parameter list</option>
+            </param>
+            <when value="preSet" />
+            <!-- Full/advanced parameters. -->
+            <when value="full">
+                 <!-- Indexing parameters -->
+                  <param name="k" type="text" value="13" label="k-mer length for the index" />
+                  <param name="s" type="text"  value="2" label="step size for the index" /> 
+                  <!-- Alignment Scoring -->
+                 <param name="t" type="text" value="99" label="maximum alignment score" />
+                 <param name="g" type="text"  value="40" label="Gap opening penalty" /> 
+                 <param name="x" type="text" value="6" label="Gap extending penalty" />
+                 <!--  Read preprocessing -->
+                 <param name="n" type="text" value="80" label="Truncate read to specified length" />
+                 <!--  Quality control -->
+                 <param name="l" type="text" value="50" label="minimum number of good quality bases" />
+                 <param name="m" type="text"  value="20" label="Repeat filter" /> 
+                 <param name="H" type="text" value="2" label="Hard clip 3' bases" />
+                 <param name="pairedEnd" type="select" label="Paired End" >
+              		<option value="mp">MP</option>
+              		<option value="pe">PE</option>
+              		<option value="pp">++</option>
+              		<option value="pn">+-</option>
+              		<option value="np">-+</option>
+          	 </param>
+
+          	 <param name="i" type="text" value="200" label="Insert size" />
+          	 <param name="d" type="text" value="50" label="standard deviation" />
+                 
+           </when>  <!-- full -->
+      </conditional>  <!-- params -->
+
+
+</inputs>
+   <outputs>
+    	<data format="txt" name="output" label="${tool.name} on ${on_string}:"/>
+   </outputs>
+   <help>
+
+**Novoalign**
+
+Novoalign is highly accurate program for mapping next-generation sequencing reads to a reference database. (http://www.novocraft.com/). Selected parameters used here are listed here.
+
+------
+
+**Indexing usage**
+
+novoindex options indexfile sequencefiles
+
+------
+
+**Options - Description**
+
+-­k 99
+
+k­mer length to be used for the index. Novoindex will select appropriate values if either of these is not specified. Default value is log4(N/20s) where N is genome size and s step size.
+
+-s 9
+
+step size for the index. Typical values are from 1 to 3, usually defaults to 1 or 2.  Genomes larger than 4Gbp can be indexed using a stepsize > 1, the requirement is N/s less than 4G.
+
+------
+
+**Alignment usage**
+
+ novoalign options
+
+------
+
+**Options - Description**
+
+-d dbname    
+  
+Full pathname of indexed reference sequence from novoindex
+
+-f read1 read2    
+
+Filenames for the read sequences for Side 1 and 2.
+
+-­t 99
+
+Sets absolute threshold or highest alignment score acceptable for the best alignment.
+
+-g 99
+
+Sets the gap opening penalty. Default 40
+
+-­x 99
+
+Sets the gap extend penalty. Default 6
+
+-­l 99
+
+Sets the minimum number of good quality bases for a read. 
+
+-­H [99]
+
+Hard clips 3' bases with quality &lt;=[99] from reads before aligning them.
+
+
+
+</help>
+
+</tool>
+
+
+
+
+