--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/signature.xml	Mon Nov 03 10:29:28 2014 -0500
@@ -0,0 +1,153 @@
+<tool id="signature" name="Small RNA Signatures" version="2.0.0">
+	<description></description>
+	<requirements>
+        	<requirement type="package" version="0.12.7">bowtie</requirement>
+        	<requirement type="package" version="0.1.18">samtools</requirement>
+        	<requirement type="package" version="0.7.7">pysam</requirement>
+        	<requirement type="package" version="2.14">biocbasics</requirement>
+        	<requirement type="package" version="3.0.3">R</requirement>
+	</requirements>
+	<command interpreter="python">
+           signature.py
+           --input $refGenomeSource.input
+           --inputFormat $refGenomeSource.input.ext
+           --minquery $minquery
+           --maxquery $maxquery
+           --mintarget $mintarget
+           --maxtarget $maxtarget
+           --minscope $minscope
+           --maxscope $maxscope
+           --outputOverlapDataframe $output
+          #if $refGenomeSource.genomeSource == "history":
+            --referenceGenome $refGenomeSource.ownFile
+          #else:
+            #silent reference= filter( lambda x: str( x[0] ) == str( $input.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1]
+            --referenceGenome $reference
+            --extract_index
+          #end if
+	  --graph $graph_type 
+          --rcode $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("${output}", header=TRUE)
+        signaturez=(signature[,2] -mean(signature[,2]))/sd(signature[,2])
+        YLIM=max(signature[,2])
+
+        ## Open output2 PDF file
+        pdf( "${output2}" )
+        par(mfrow=c(2,2),oma = c(0, 0, 3, 0))
+
+        plot(signature[,1:2], type = "h", main="Numbers of pairs", cex.main=1, xlab="overlap (nt)", ylim=c(0,YLIM), ylab="Numbers of pairs", col="darkslateblue", lwd=4)
+
+        plot(signaturez, type = "l", main="Number of pairs Z-scores", cex.main=1, xlab="overlap (nt)", ylab="z-score", pch=19, cex=0.2, col="darkslateblue", lwd=2, cex.lab=1, cex.axis=1, xaxt="n")
+        axis(1, at=seq(from=1, to=length(signature[,1]), by=3) )
+
+        plot(signature[,1], signature[,3]*100, type = "l", main="Overlap probabilities",
+             cex.main=1, xlab="overlap (nt)", ylab="Probability [%]", ylim=c(0,50),
+             pch=19, col="darkslateblue", lwd=2, cex.lab=1, cex.axis=1, xaxt="n")
+        axis(1, at=seq(from=1, to=length(signature[,1]), by=3) )
+
+        overlap_prob_z=(signature[,3] -mean(signature[,3]))/sd(signature[,3])
+        plot(overlap_prob_z, type = "l", main="Overlap Probability Z-scores", cex.main=1, xlab="overlap (nt)", ylab="z-score", pch=19, cex=0.2, col="darkslateblue", lwd=2, cex.lab=1, cex.axis=1, xaxt="n")
+        axis(1, at=seq(from=1, to=length(signature[,1]), by=3) )
+        
+        mtext("Overlap Signatures of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs", outer = TRUE, cex=1)
+        devname = dev.off()
+        ## Close the PDF file
+      }
+
+      treillisgraph = function () {
+        ## Open output2 PDF file
+        pdf( "${output2}", paper="special", height=11.69, width=8.2677 )
+        signature = read.delim("${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="Overlap probabilities"/>
+        </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>
+
+  <test>
+      <param name="genomeSource" value="history" />
+      <param name="ownFile" value ="transposons.fasta" ftype="fasta" />
+      <param name="input" value="sr_bowtie.output" ftype="tabular" />
+      <param name="minquery" value="23" />
+      <param name="maxquery" value="29" />
+      <param name="mintarget" value="23" />
+      <param name="maxtarget" value="29" />
+      <param name="minscope" value="1" />
+      <param name="maxscope" value="26" />
+      <param name="graph_type" value="global" />
+      <output name="readmap_dataframe" ftype="tabular" value="signature_data_frame.tab"/>
+      <output name="readmap_PDF" ftype="pdf" value="Overlap_probabilities.pdf"/>
+  </test>
+
+
+
+</tool>
+