--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/signature.xml	Wed Oct 21 11:35:25 2015 -0400
@@ -0,0 +1,149 @@
+<tool id="signature" name="Small RNA Signatures" version="2.0.5">
+    <description />
+    <requirements>
+        <requirement type="package" version="0.12.7">bowtie</requirement>
+        <requirement type="package" version="0.7.7">pysam</requirement>
+        <requirement type="package" version="3.1.2">R</requirement>
+        <requirement type="package" version="2.14">biocbasics</requirement>
+        <requirement type="package" version="1.9">numpy</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 help="Built-ins were indexed using default options" label="Will you select a reference genome from your history or use a built-in index?" name="genomeSource" type="select">
+                <option value="indexed">Use a built-in index</option>
+                <option value="history">Use one from the history</option>
+            </param>
+            <when value="indexed">
+                <param format="tabular,sam,bam" label="Compute signature from this bowtie standard output" name="input" type="data">
+                    <validator message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history." metadata_column="0" metadata_name="dbkey" table_name="bowtie_indexes" type="dataset_metadata_in_data_table" />
+                </param>
+            </when>
+            <when value="history">
+                <param format="fasta" label="Select the fasta reference" name="ownFile" type="data" />
+                <param format="tabular,sam,bam" label="Compute signature from this bowtie standard output" name="input" type="data" />
+            </when>
+        </conditional>
+        <param help="'23' = 23 nucleotides" label="Min size of query small RNAs" name="minquery" size="3" type="integer" value="23" />
+        <param help="'29' = 29 nucleotides" label="Max size of query small RNAs" name="maxquery" size="3" type="integer" value="29" />
+        <param help="'23' = 23 nucleotides" label="Min size of target small RNAs" name="mintarget" size="3" type="integer" value="23" />
+        <param help="'29' = 29 nucleotides" label="Max size of target small RNAs" name="maxtarget" size="3" type="integer" value="29" />
+        <param help="'1' = 1 nucleotide overlap" label="Minimal relative overlap analyzed" name="minscope" size="3" type="integer" value="1" />
+        <param help="'1' = 1 nucleotide overlap" label="Maximal relative overlap analyzed" name="maxscope" size="3" type="integer" value="26" />
+        <param help="Signature can be computed globally or by item present in the alignment file" label="Graph type" name="graph_type" type="select">
+            <option selected="True" value="global">Global</option>
+            <option value="lattice">Lattice</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="tabular" label="signature data frame" name="output" />
+        <data format="pdf" label="Overlap probabilities" name="output2" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="genomeSource" value="history" />
+            <param ftype="fasta" name="ownFile" value="ensembl.fa" />
+            <param ftype="bam" name="input" value="sr_bowtie.bam" />
+            <param name="minquery" value="23" />
+            <param name="maxquery" value="29" />
+            <param name="mintarget" value="23" />
+            <param name="maxtarget" value="29" />
+            <param name="minscope" value="5" />
+            <param name="maxscope" value="15" />
+            <param name="graph_type" value="global" />
+            <output file="signature.tab" ftype="tabular" name="output" />
+            <output file="signature.pdf" ftype="pdf" name="output2" />
+        </test>
+    </tests>
+    <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>
+    <citations>
+            <citation type="doi">10.1007/978-1-4939-0931-5_12</citation>
+    </citations>
+    <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("${output}", header=TRUE)
+        signaturez=data.frame(signature[,1], (signature[,2] -mean(signature[,2]))/sd(signature[,2]))
+        overlap_prob_z=data.frame(signature[,1], (signature[,3] -mean(signature[,3]))/sd(signature[,3]))
+        YLIM=max(signature[,2])
+        
+
+        ## Open output2 PDF file
+        pdf( "${output2}" )
+        if (YLIM!=0) {
+          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)
+
+          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)
+
+          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)
+
+          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(${minscope},${maxscope}), 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>
+</tool>