--- a/Codonlogo.xml	Mon Jan 16 07:03:36 2012 -0500
+++ b/Codonlogo.xml	Fri Jan 20 09:03:40 2012 -0500
@@ -1,27 +1,37 @@
 <tool id="codonlogo" name="Codon Logo" version="3">
   <description>generator for fasta (eg Clustal alignments)</description>
-  <command interpreter="python -W ignore::DeprecationWarning"> 
-    codonlogo -F $outformat -s $size -f $input -o $output -t "$logoname" -m $frame -n $stacks -X $showxaxis --show-yaxis $showyaxis --errorbars $errorbars 
+  <command interpreter="/usr/tmp/bin/python2.7 -W ignore::DeprecationWarning"> 
+    codonlogo -F $outformat -s $size -f $input -o $output -t "$logoname" -m $frame -n $stacks -X $showxaxis --show-yaxis $showyaxis --errorbars $errorbars -G $strict --fineprint "$fineprint" --stack-width $stackwidth --stack-height $stackheight --box $box --resolution $resolution --scale-width $scalewidth
 
     #if str($ylabel) != ''
-    -x $xlabel 
+    -x "$xlabel" 
     #end if
     
     #if str( $ylabel) != ''
-    -y $ylabel 
+    -y "$ylabel"
     #end if
-    #if $range.mode == 'part'
+    
+    #if str($range.mode) == 'part'
     -l "$range.seqstart" -u "$range.seqend" 
     #end if
-    #if $comp.mode == 'equiprobable'
+    #if str($comp.mode) == 'equiprobable'
     --composition 'equiprobable' 
     #end if
-    #if $comp.mode == 'none'
+    #if str($comp.mode) == 'none'
     --composition 'none' 
     #end if
-    #if $comp.mode == 'file'
+    #if str($comp.mode) == 'file'
     -R $compfile 
     #end if
+    #if str($comp.mode) == 'Escherichiacoli'
+    -R Escherichiacoli.txt
+    #end if
+    #if str($comp.mode) == 'Saccharomycescerevisiae'
+    -R Saccharomycescerevisiae.txt
+    #end if
+    #if str($comp.mode) == 'Homosapiens'
+    -R Homosapiens.txt
+    #end if
     
     #if $colours.colour == 'part'
     
@@ -322,7 +332,7 @@
   </command>
   <inputs>
     <page>
-      <param format="fasta" name="input" type="data" label="txt" />
+      <param format="text" name="input" type="data" label="Input file.(must be an aligned fasta file of sequences the same length, recommended to use sequences aligned by codon)" />
       
       <param name="logoname" label="Title for output Sequence Logo" type="text" size="50" value="" />
       
@@ -334,13 +344,15 @@
       <option value="eps">EPS</option>
       <option value="txt">Text (shows the detailed calculations for each position - no image)</option>
     </param>
+    <param name="resolution" size="5" type="integer" value="96" label="Bitmap resolution in dots per inch (DPI).For high quality printable PNG this should be set to 600" />
+
     <param name="frame" type="select" label="Frame to view the alignment. If reverse complement is selected then codonlogo will read from the last symbol in the sequences backwards and replace each base with it's complement." >
       <option value="0" selected="True">0</option>
       <option value="1">+1</option>
-      <option value="2">-1</option>
+      <option value="2">+2</option>
       <option value="3">reverse complement 0</option>
       <option value="4">reverse complement +1</option>
-      <option value="5">reverse complement -1</option>
+      <option value="5">reverse complement +2</option>
     </param>
     <param name="stacks" size="5" type="integer" value="20" label="Number of stacks per line, default 20" />
     <param name="showxaxis" type="select" display="radio" label="Display sequence numbers along x-axis?" >
@@ -350,9 +362,15 @@
     <param name="xlabel" label="X-axis label" type="text" size="50" value="" />
     <param name="ylabel" label="Y-axis label" type="text" size="50" value="" />
     
-    <param name="fineprint" label="The fine print." type="text" size="50" value="CodonLogo 1.0" />
+    <param name="fineprint" label="The fine print." type="text" size="50" value="CodonLogo 1.1" />
+    
+    <param name="stackwidth" size="5" type="float" value="40.0" label="Width of a logo stack" />
     
-    
+    <param name="stackheight" size="5" type="integer" value="100" label="height of a logo stack" />
+     <param name="box" type="select" display="radio" label="Draw boxes around symbols?" >
+        <option value="True" >Yes</option>
+        <option value="False" selected="True">No</option>
+      </param>
       <param name="showyaxis" type="select" display="radio" label="Display entropy scale along y-axis?" >
         <option value="True" selected="True">Yes</option>
         <option value="False">No</option>
@@ -361,6 +379,14 @@
         <option value="True" selected="True">Yes</option>
         <option value="False">No</option>
       </param>
+      <param name="scalewidth" type="select" display="radio" label="Scale the visible stack width by the fraction of symbols in the column?" >
+        <option value="True" selected="True">Yes</option>
+        <option value="False">No</option>
+      </param>
+      <param name="strict" type="select" display="radio" label="Allow gaps which are not in groups of 3/ allow codons with ambiguous nucleotides." >
+        <option value="False" selected="True">Yes</option>
+        <option value="True" >No</option>
+      </param>
   <conditional name="range">
         <param name="mode" type="select" label="Include entire sequence (default) or specify a subsequence range to use">
           <option value="complete" selected="true">complete sequence</option>
@@ -369,10 +395,10 @@
         <when value="complete">
         </when>
         <when value="part">    
-           <param name="seqstart" size="5" type="integer" value="1" help="WARNING: Specifying indexes outside the sequence lengths will cause unpredictable but bad consequences!" 
-             label="Index (eg 1=first letter) of the start of the sequence range to include in the logo">
+           <param name="seqstart" size="5" type="integer" value="1" help="WARNING: Specifying codon numbers outside the sequence lengths will cause unpredictable but bad consequences!" 
+             label="Index_start (eg 1=first codon) of the start of the sequence range to include in the logo">
            </param>
-           <param name="seqend" size="5" type="integer" value="99999" label="Index (eg 75=75th letter) of the end of the sequence range to include in the logo" >
+           <param name="seqend" size="5" type="integer" value="99999" label="Index_end (eg 75=75th codon) of the end of the sequence range to include in the logo" >
            </param> 
         </when>
     </conditional>
@@ -381,6 +407,9 @@
         
         <option value="equiprobable" >equiprobable</option>
         <option value="none" >none</option>
+<!--	<option value="Escherichiacoli" >Escherichiacoli</option>
+	<option value="Homosapiens" >Homosapiens</option>
+	<option value="Saccharomycescerevisiae" >Saccharomycescerevisiae</option>-->
         <option value="file">from file</option>
         
       </param>