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+++ b/signature.xml	Mon Aug 28 09:29:47 2017 -0400
@@ -0,0 +1,119 @@
+<tool id="signature" name="Small RNA Signatures" version="3.0.0">
+    <description />
+    <requirements>
+        <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
+        <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
+        <requirement type="package" version="1.3.2=r3.3.1_0">r-optparse</requirement>
+        <requirement type="package" version="0.6_28=r3.3.1_0">r-latticeextra</requirement>
+        <requirement type="package" version="2.2.1=r3.3.1_0">r-gridextra</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Tool exception" />
+    </stdio>
+      <command detect_errors="exit_code"><![CDATA[
+        samtools index '$input' &&
+        python '$__tool_directory__'/signature.py
+           --input '$input'
+           --minquery '$minquery'
+           --maxquery '$maxquery'
+           --mintarget '$mintarget'
+           --maxtarget '$maxtarget'
+           --minscope '$minscope'
+           --maxscope '$maxscope'
+           --output_h '$h_dataframe'
+           --output_z '$z_dataframe' &&
+        Rscript '$__tool_directory__'/signature.r
+           --h_dataframe '$h_dataframe'
+           --z_dataframe '$z_dataframe'
+           --plot_method '$plot_method'
+           --pdf '$pdf'
+           --title "Overlap Signatures of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs"
+    ]]></command>
+    <inputs>
+        <param format="bam" label="Compute signature from this bowtie standard output" name="input" type="data" />
+        <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="plot_method" type="select">
+            <option selected="True" value="global">Global</option>
+            <option value="lattice">Lattice</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="tabular" label="z-signature data frame" name="z_dataframe">
+            <actions>
+                <action name="column_names" type="metadata" default="Chromosome,Overlap,Number_of_pairs,z-score" />
+            </actions>
+        </data>
+        <data format="tabular" label="h-signature data frame" name="h_dataframe">
+            <actions>
+                <action name="column_names" type="metadata" default="Chromosome,Overlap,overlap_probability,z-score" />
+            </actions>
+        </data>
+        <data format="pdf" label="Overlap probabilities" name="pdf" />
+    </outputs>
+    <tests>
+        <test>
+            <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="plot_method" value="global" />
+            <output file="h.tab" ftype="tabular" name="h_dataframe" />
+            <output file="z.tab" ftype="tabular" name="z_dataframe" />
+            <output file="global.pdf" ftype="pdf" name="pdf" />
+        </test>
+        <test>
+            <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="plot_method" value="lattice" />
+            <output file="h.tab" ftype="tabular" name="h_dataframe" />
+            <output file="z.tab" ftype="tabular" name="z_dataframe" />
+            <output file="lattice.pdf" ftype="pdf" name="pdf" />
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
+Compute small RNA (piRNA, siRNA, ...) signatures.
+
+This tool computes (i) the number of pairs by overlap classes (in nt) and associated the z-scores,
+and (ii) the ping-pong signal (`Brennecke et al, 2009`_) and associated z-scores. 
+Options set the min and max size of both the query small rna class and the target small rna class, 
+the range over which to compute the signatures, and whether the signatures should be reported at 
+genome-wide level or by item (chromosomes, genes, etc.). For details on computational algorithmes 
+for piRNA and siRNA signatures, see `Antoniewski (2014)`_.
+
+.. _Brennecke et al, 2009: http://dx.doi.org/10.1126/science.1165171
+.. _Antoniewski (2014): https://link.springer.com/protocol/10.1007%2F978-1-4939-0931-5_12
+
+**Input**
+
+A **sorted** BAM alignment file.
+
+**Outputs**
+
+**Global**: The number of pairs founds, the ping-pong signal and the associated z-scores 
+are computed at genome-wide level and returned in a pdf file.
+
+**Lattice**: The number of pairs founds, the ping-pong signals and the associated z-scores 
+are computed for each items described in the BAM alignment input and returned in a pdf file as a lattice graph.
+
+
+        </help>
+    <citations>
+            <citation type="doi">10.1007/978-1-4939-0931-5_12</citation>
+    </citations>
+</tool>