--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/piRNAsignature.xml	Mon Jun 23 04:09:27 2014 -0400
@@ -0,0 +1,122 @@
+<tool id="piRNAsignature" name="piRNA Signatures" version="1.0.1">
+	<description></description>
+	<command interpreter="python">
+          piRNAsignature.py $refGenomeSource.input $refGenomeSource.input.ext $minquery $maxquery $mintarget $maxtarget $minscope $maxscope $output
+          #if $refGenomeSource.genomeSource == "history":
+            $refGenomeSource.ownFile
+            --do_not_extract_index
+          #else:
+            #silent reference= filter( lambda x: str( x[0] ) == str( $input.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1]
+            $reference
+            --extract_index
+          #end if
+	  $graph_type 
+          $sigplotter
+       </command>
+
+	<inputs>
+          <conditional name="refGenomeSource">
+             <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
+               <option value="indexed">Use a built-in index</option>
+               <option value="history">Use one from the history</option>
+             </param>
+	     <when value="indexed">
+  	        <param name="input" type="data" format="tabular,sam,bam" label="Compute signature from this bowtie standard output">
+		  <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/>
+	        </param>
+	     </when>
+             <when value="history">
+                <param name="ownFile" type="data" format="fasta"  label="Select the fasta reference" />
+  	        <param name="input" type="data" format="tabular,sam,bam" label="Compute signature from this bowtie standard output"/>
+             </when>
+          </conditional>  <!-- refGenomeSource -->
+		<param name="minquery" type="integer" size="3" value="23" label="Min size of query small RNAs" help="'23' = 23 nucleotides"/>
+		<param name="maxquery" type="integer" size="3" value="29" label="Max size of query small RNAs" help="'29' = 29 nucleotides"/>
+                <param name="mintarget" type="integer" size="3" value="23" label="Min size of target small RNAs" help="'23' = 23 nucleotides"/>
+                <param name="maxtarget" type="integer" size="3" value="29" label="Max size of target small RNAs" help="'29' = 29 nucleotides"/>
+                <param name="minscope" type="integer" size="3" value="1" label="Minimal relative overlap analyzed" help="'1' = 1 nucleotide overlap"/>
+                <param name="maxscope" type="integer" size="3" value="26" label="Maximal relative overlap analyzed" help="'1' = 1 nucleotide overlap"/>
+		<param name="graph_type" type="select" label="Graph type" help="Signature can be computed globally or by item present in the alignment file">
+		  <option value="global" selected="True">Global</option>
+                  <option value="lattice">Lattice</option>
+		</param>
+	</inputs>
+
+  <configfiles>
+    <configfile name="sigplotter">
+      graph_type = "${graph_type}"
+
+      globalgraph = function () {
+        ## Setup R error handling to go to stderr
+        options( show.error.messages=F,
+                 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+        signature = read.delim("${output}", header=TRUE)
+        ## Open output1 PDF file
+        pdf( "${output1}" )
+        signaturez=(signature[,2] -mean(signature[,2]))/sd(signature[,2])
+        plot(signaturez, type = "b", main="signature", cex.main=2, xlab="overlap (nt)", ylab="z-score", pch=19, cex=0.8, col="darkslateblue", lwd=3, cex.lab=1.5, cex.axis=1.4, xaxt="n")
+        axis(1, at=seq(from=1, to=length(signature[,1]), by=3) )
+        devname = dev.off()
+        ## Close the PDF file
+        ## Open output2 PDF file
+        pdf( "${output2}" )
+        YLIM=max(signature[,2])
+        plot(signature[,1:2], type = "h", xlab="overlap (nt)", ylim=c(0,YLIM), ylab="number of pairs", col="darkslateblue", lwd=7)
+        devname = dev.off()
+        ## Close the PDF file
+        ## Open output3 PDF file
+        pdf( "${output3}" )
+        plot(signature[,1], signature[,3]*100, type = "l", main="ping-pong Signature of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs",
+             cex.main=1, xlab="overlap (nt)", ylab="ping-pong signal [%]", ylim=c(0,50),
+             pch=19, col="darkslateblue", lwd =4, cex.lab=1.2, cex.axis=1, xaxt="n")
+        axis(1, at=seq(from=1, to=length(signature[,1]), by=3) )
+        devname = dev.off()
+        ## Close the PDF file
+      }
+
+      treillisgraph = function () {
+        ## Open output3 PDF file
+        pdf( "${output3}", paper="special", height=11.69, width=8.2677 )
+        signature = read.delim("${output}", header=TRUE)
+        options( show.error.messages=F,
+               error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+        library(lattice)
+        print (xyplot(signature[,3]*100~signature[,1]|signature[,4], type = "l", xlim=c(1,26), main="ping-pong Signature of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs",
+             par.strip.text=list(cex=.5), strip=strip.custom(which.given=1, bg="lightblue"), scales=list(cex=0.5),
+             cex.main=1, cex=.5, xlab="overlap (nt)", ylab="ping-pong signal [%]",
+             pch=19, col="darkslateblue", lwd =1.5, cex.lab=1.2, cex.axis=1.2,
+             layout=c(4,12), as.table=TRUE, newpage = T) )
+        devnname = dev.off()
+      }
+
+      if (graph_type=="global") {
+	globalgraph()
+
+      }
+      if(graph_type=="lattice") {
+        treillisgraph()
+      }
+    </configfile>
+  </configfiles>
+
+        <outputs>
+                <data name="output" format="tabular" label = "signature data frame"/>
+                <data name="output2" format="pdf" label="number of pairs signature">
+                <filter>(graph_type == "global")</filter>
+                </data>
+                <data name="output1" format="pdf" label="z-score signature">
+                <filter>(graph_type == "global")</filter>
+                </data>
+                <data name="output3" format="pdf" label="ping-pong signal (hannon algo.)"/>
+        </outputs>
+
+        <help>
+
+**What it does**
+
+This tool computes the number of pairs by overlap classes (in nt) from a bowtie output file, the z-score calculated from these numbers of pairs, and the ping-pong signal as described in Brennecke et al (2009) Science.
+The numerical options set the min and max size of both the query small rna class and the target small rna class
+Three type of signals are plotted in separate pdf files, the number of pairs founds, the z-score calculated from these numbers of pairs, and the ping-pong signal as described in Brennecke et al (2009) Science.
+
+        </help>
+</tool>