--- a/signature.xml	Sat Feb 25 09:54:28 2023 +0000
+++ b/signature.xml	Thu Apr 06 23:00:54 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="signature" name="Small RNA Signatures" version="3.4.2>">
+<tool id="signature" name="Small RNA Signatures" version="3.5.0">
     <description />
     <requirements>
         <requirement type="package" version="1.23.4">numpy</requirement>
@@ -26,9 +26,15 @@
         Rscript '$__tool_directory__'/signature.r
            --h_dataframe '$h_dataframe'
            --z_dataframe '$z_dataframe'
-           --plot_method '$plot_method'
+           --plot_method '$plot_options.plot_method'
            --pdf '$pdf'
            --title "Overlap Signatures of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs"
+           #if $plot_options.plot_method == "global":
+               --npairs_ylim $plot_options.npairs_ylim
+               --npairszscore_ylim $plot_options.npairszscore_ylim
+               --overlapprob_ylim $plot_options.overlapprob_ylim
+               --overlapprobzscore_ylim $plot_options.overlapprobzscore_ylim
+            #end if
     ]]></command>
     <inputs>
         <param format="bam" label="Compute signature from this bowtie standard output" name="input" type="data" />
@@ -38,10 +44,27 @@
         <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>
+        <conditional name="plot_options">
+            <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>
+            <when value="lattice" />
+            <when value="global">
+                <param name="npairs_ylim" type="integer" value="0" optional="true"
+                       label="Maximum of Y-scale of the Numbers-of-pairs plot"
+                       help="Interger. Leave 0 for self-determination of Y-scale" />
+                <param name="npairszscore_ylim" type="integer" value="0" optional="true"
+                       label="Maximum of Y-scale of the Number-of-pairs-Z−scores plot"
+                       help="Integer. Leave 0 for self-determination of Y-scale" />
+                <param name="overlapprob_ylim" type="integer" value="0" optional="true"
+                       label="Maximum of Y-scale of the Overlap-probabilities plot"
+                       help="Percent value as an Integer. Leave 0 for self-determination of % Y-scale" />
+                <param name="overlapprobzscore_ylim" type="integer" value="0" optional="true"
+                       label="Maximum of Y-scale of the Overlap-probabilities-Z−scores plot"
+                       help="Interger. Leave 0 for self-determination of Y-scale" />
+            </when>
+        </conditional>
     </inputs>
     <outputs>
         <data format="tabular" label="z-signature data frame" name="z_dataframe">
@@ -65,11 +88,14 @@
             <param name="maxtarget" value="29" />
             <param name="minscope" value="5" />
             <param name="maxscope" value="15" />
-            <param name="plot_method" value="global" />
+            <conditional name="plot_options">
+                <param name="plot_method" value="global" />
+            </conditional>
             <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" />
@@ -78,7 +104,30 @@
             <param name="maxtarget" value="29" />
             <param name="minscope" value="5" />
             <param name="maxscope" value="15" />
-            <param name="plot_method" value="lattice" />
+            <conditional name="plot_options">
+                <param name="plot_method" value="global" />
+            </conditional>
+            <param name="npairs_ylim" value="100" />
+            <param name="npairszscore_ylim" value="0" />
+            <param name="overlapprob_ylim" value="1" />
+            <param name="overlapprobzscore_ylim" value="4" />
+
+            <output file="h.tab" ftype="tabular" name="h_dataframe" />
+            <output file="z.tab" ftype="tabular" name="z_dataframe" />
+            <output file="global-limited.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" />
+            <conditional name="plot_options">
+                <param name="plot_method" value="lattice" />
+            </conditional>
             <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" />