--- a/edge_pro.xml	Fri Jan 31 05:44:03 2014 -0500
+++ b/edge_pro.xml	Wed Mar 05 06:44:35 2014 -0500
@@ -1,54 +1,52 @@
-<tool id="edge_pro" name="EDGE-pro" version="1.0.0">
+<tool id="edge_pro" name="EDGE-pro" version="1.0.1">
   <description>Gene expression in Prokaryotes</description>
   <requirements>
     <requirement type="package" version="2.1.0">bowtie2</requirement>
     <requirement type="package" version="1.3.1">edge-pro</requirement>
   </requirements>
-  <command interpreter="python">
-    edge_pro.py
-    --num-threads=\${GALAXY_SLOTS:-4}
-    
+  <command>
+    edge.pl -t \${GALAXY_SLOTS:-4} -o edge_out
     ## Mandatory input parameters
-    --genome $genome
-    --ptt $ptt
-    --rnt $rnt
+    -g $genome
+    -p $ptt
+    -r $rnt
     ## First input file always required
-    --input1 $singlePaired.input1
+    -u $singlePaired.input1
     ## Second input only if input is paired-end
     #if $singlePaired.sPaired == "paired"
-      --input2=$singlePaired.input2
+      -v $singlePaired.input2
+      #if str($singlePaired.minInsertSize)
+        -m $singlePaired.minInsertSize
+      #end if
+      #if str($singlePaired.maxInsertSize)
+        -M $singlePaired.maxInsertSize
+      #end if
     #end if
     
     ## Optional input parameters
     #if $params.settingsType == "full"
-      #if str($params.minInsertSize)
-        --minInsertSize=$params.minInsertSize
-      #end if
-      #if str($params.maxInsertSize)
-        --maxInsertSize=$params.maxInsertSize
-      #end if
       #if str($params.window)
-        --window=$params.window
+        -w $params.window
       #end if
       #if str($params.utrSize)
-        --utrSize=$params.utrSize
+        -i $params.utrSize
       #end if
       #if str($params.similarity)
-        --similarity=$params.similarity
+        -x $params.similarity
       #end if
       #if str($params.readLength)
-        --readLength=$params.readLength
+        -l $params.readLength
       #end if
       #if str($params.minCoverage)
-        --minCoverage=$params.minCoverage
+        -c $params.minCoverage
       #end if
     #end if
-    
-    ## Outputs
-    --out-aln $out_aln
-    --out-rpkm $out_rpkm
-    --out-log $out_log
+    &gt; $out_log 2&gt;&amp;1 ## need to redirect stderr because edge.pl calls bowtie2 and count which write some logging info there
+    &amp;&amp; cat edge_out.rpkm_* > $out_rpkm
   </command>
+  <stdio>
+    <exit_code range="1:" level="fatal" />
+  </stdio>
   <inputs>
     <conditional name="singlePaired">
       <param name="sPaired" type="select" label="Is this library mate-paired?">
@@ -61,6 +59,8 @@
       <when value="paired">
         <param format="fastqsanger" name="input1" type="data" label="Forward FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" />
         <param format="fastqsanger" name="input2" type="data" label="Reverse FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" />
+        <param name="minInsertSize" type="integer" optional="true" min="0" value="0" label="Minimun insert size in paired-end library for Bowtie2 (-m)" />
+        <param name="maxInsertSize" type="integer" optional="true" min="1" value="500" label="Maximun insert size in paired-end library for Bowtie2 (-M)" />
       </when>
     </conditional>
     
@@ -70,25 +70,22 @@
     
     <conditional name="params">
       <param name="settingsType" type="select" label="Parameter settings" help="For most needs, use default settings. If you want full control use Full Parameter List">
-        <option value="preSet">Use Defaults</option>
+        <option value="preSet">Use defaults</option>
         <option value="full">Full parameter list</option>
       </param>
       <when value="preSet" />
-      <!-- Full/advanced params. -->
       <when value="full">
-        <param name="minInsertSize" type="integer" optional="true" value="0" label="Minimun insert size for a read pair (-m)" help="For paired-end reads only" />
-        <param name="maxInsertSize" type="integer" optional="true" value="500" label="Maximun insert size for a read pair (-M)" help="For paired-end reads only" />
         <param name="window" type="integer" optional="true" value="100" label="Window length for coverage distribution (-w)" help="Used to distribute the coverage between two overlapping genes. See help below for details" />
         <param name="utrSize" type="integer" optional="true" value="40" label="Size of the untranslated region (-i)" help="Enter the size of the untranslated region between the initial transcription site and the start codon" />
         <param name="similarity" type="float" optional="true" value="0.15" label="Percentage for similar coverage (-x)" help="Enter the percentage used to determine when two coverage values are considered similar. See help below for details" />
         <param name="readLength" type="integer" optional="true" value="" label="Read length (-l)" help="If not specified, the first 1000 reads are used to approximate the read length" />
         <param name="minCoverage" type="integer" optional="true" value="3" label="Minimum average coverage for expressed genes (-c)" help="Coverage less than specified is assumed to be noise and gene is considered to not be expressed" />
-      </when> <!-- full -->
+      </when>
     </conditional>
   </inputs>
 
   <outputs>
-    <data format="sam" name="out_aln" label="${tool.name} on ${on_string}: alignment"/>
+    <data format="sam" name="out_aln" label="${tool.name} on ${on_string}: alignment" from_work_dir="edge_out.alignments" />
     <data format="tabular" name="out_rpkm" label="${tool.name} on ${on_string}: rpkm"/>
     <data format="txt" name="out_log" label="${tool.name} on ${on_string}: log"/>
   </outputs>
@@ -122,7 +119,7 @@
 
 If you use this tool in Galaxy, please cite |Cuccuru2013|_.
 
-.. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted*
+.. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics*, accepted
 .. _Cuccuru2013: http://orione.crs4.it/
 
 This tool uses `EDGE-pro`_, which is licensed separately. Please cite |Magoc2013|_.