--- a/rgWebLogo3.xml	Thu Dec 03 15:55:38 2015 -0500
+++ b/rgWebLogo3.xml	Fri Nov 17 10:19:39 2017 -0500
@@ -1,106 +1,104 @@
-<tool id="rgweblogo3" name="Sequence Logo" version="0.4">
-   <description>generator for fasta (eg Clustal alignments)</description>
-   <requirements>
-      <requirement type="package" version="1.7.1">numpy</requirement>
-      <requirement type="package" version="3.3">weblogo</requirement>
-      <requirement type="package" version="9.10">ghostscript</requirement>
-   </requirements>
-   <command interpreter="python"> 
-    rgWebLogo3.py -F $outformat -s $size -i $input -o $output -t "$logoname" -c "$colours" -U "$units"
-#if $range.mode == 'part'
--l "$range.seqstart" -u "$range.seqend"
-#end if
-    </command>
-  <inputs>
-   <page>
-    <param format="fasta" name="input" type="data" label="Fasta File" />
-    <param name="logoname" label="Title for output Sequence Logo" type="text" value="Galaxy-Rgenetics Sequence Logo" />
-    <param name="outformat" type="select" label="Output format for image (or text report)" >
-      <option value="png" selected="True">PNG screen quality</option>
-      <option value="png_print">High quality printable PNG</option>
-      <option value="pdf">PDF</option>
-      <option value="jpeg">JPG</option>
-      <option value="eps">EPS</option>
-      <option value="logodata">Text (shows the detailed calculations for each position - no image)</option>
-    </param>
-    <param name="units" type="select" label="Display Units"
-      help="What the height of each logo element depicts - eg bits of entropy (default)">
-      <option value="bits" selected="True">Entropy (bits)</option>
-      <option value="probability">Probability</option>
-      <option value="nats">Nats</option>
-      <option value="kT">kT</option>
-      <option value="kJ/mol">kJ/mol</option>
-      <option value="kcal/mol">kcal/mol</option>
-    </param>
-    <param name="colours" type="select" label="Colour scheme for output Sequence Logo" 
-      help="Note that some of these only make sense for protein sequences!">
-      <option value="auto" selected="True">Default automatic colour selection</option>
-      <option value="base pairing">Base pairing</option>
-      <option value="charge">Charge colours</option>
-      <option value="chemistry">Chemistry colours</option>
-      <option value="classic">Classical colours</option>
-      <option value="hydrophobicity">Hydrophobicity</option>
-      <option value="monochrome">monochrome</option>
-    </param>
+<tool id="rgweblogo3" name="Sequence Logo" version="3.5.0">
+    <description>generator for fasta (eg Clustal alignments)</description>
+    <requirements>
+        <requirement type="package" version="3.5.0">weblogo</requirement>
+    </requirements>
+    <command><![CDATA[
+        python '$__tool_directory__/rgWebLogo3.py'
+            -F $outformat
+            -s $size
+            -i '$input'
+            -o '$output'
+            -t '$logoname'
+            -c '$colours'
+            -U '$units'
 
-    
-    <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>
-          <option value="part">Only use a part of the sequence</option>
+        #if $range.mode == 'part'
+            -l '$range.seqstart' -u '$range.seqend'
+        #end if
+    ]]></command>
+    <inputs>
+        <param format="fasta" name="input" type="data" label="Fasta File" />
+        <param name="logoname" label="Title for output Sequence Logo" type="text" value="Galaxy-Rgenetics Sequence Logo" />
+        <param name="outformat" type="select" label="Output format for image (or text report)" >
+            <option value="png" selected="True">PNG screen quality</option>
+            <option value="png_print">High quality printable PNG</option>
+            <option value="pdf">PDF</option>
+            <option value="jpeg">JPG</option>
+            <option value="eps">EPS</option>
+            <option value="logodata">Text (shows the detailed calculations for each position - no image)</option>
+        </param>
+        <param name="units" type="select" label="Display Units" help="What the height of each logo element depicts - eg bits of entropy (default)">
+            <option value="bits" selected="True">Entropy (bits)</option>
+            <option value="probability">Probability</option>
+            <option value="nats">Nats</option>
+            <option value="kT">kT</option>
+            <option value="kJ/mol">kJ/mol</option>
+            <option value="kcal/mol">kcal/mol</option>
+        </param>
+        <param name="colours" type="select" label="Colour scheme for output Sequence Logo"
+        help="Note that some of these only make sense for protein sequences!">
+            <option value="auto" selected="True">Default automatic colour selection</option>
+            <option value="base pairing">Base pairing</option>
+            <option value="charge">Charge colours</option>
+            <option value="chemistry">Chemistry colours</option>
+            <option value="classic">Classical colours</option>
+            <option value="hydrophobicity">Hydrophobicity</option>
+            <option value="monochrome">monochrome</option>
         </param>
-        <when value="complete">
-        </when>
-        <when value="part">    
-           <param name="seqstart" 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>
-           <param name="seqend" type="integer" value="99999" label="Index (eg 75=75th letter) of the end of the sequence range to include in the logo" >
-           </param> 
-        </when>
-    </conditional>
-    <param name="size" type="select" label="Output weblogo size" >
-      <option value="large" selected="True">Large</option>
-      <option value="medium">Medium</option>
-      <option value="small">Small</option>
-    </param>
-   </page>
-  </inputs>
-  <outputs>
-    <data format="pdf" name="output"  label="${logoname}_output.${outformat}">
-       <change_format>
-           <when input="outformat" value="png_print" format="png" />
-           <when input="outformat" value="png" format="png" />
-           <when input="outformat" value="jpeg" format="jpg" />
-           <when input="outformat" value="eps" format="eps" />
-           <when input="outformat" value="logodata" format="txt" />
-       </change_format>
-    </data>
-  </outputs>
-  <tests>
-    <test>  
-      <param name="input" value="rgClustal_testout.fasta" />
-      <param name="logoname" value="Galaxy/Rgenetics weblogo" />
-      <param name="outformat" value="jpeg" />
-      <param name="mode" value="complete" />
-      <param name="size" value="medium" />      
-      <param name="colours" value="auto" />
-      <param name="units" value="bits" /> 
-      <output name="output" file="rgWebLogo3_test.jpg" ftype="jpg" compare="sim_size" delta="10000" />
-    </test>
-    <test>  
-      <param name="input" value="rgClustal_testout.fasta" />
-      <param name="logoname" value="Galaxy/Rgenetics weblogo" />
-      <param name="outformat" value="png" />
-      <param name="mode" value="complete" />
-      <param name="size" value="medium" />      
-      <param name="colours" value="auto" />
-      <param name="units" value="probability" /> 
-      <output name="output" file="rgWebLogo3_test2.png" ftype="png" compare="sim_size" delta="10000" />
-    </test>
-  </tests>
-  <help>
 
+        <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>
+                <option value="part">Only use a part of the sequence</option>
+            </param>
+            <when value="complete" />
+            <when value="part">
+                <param name="seqstart" 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="seqend" type="integer" value="99999" label="Index (eg 75=75th letter) of the end of the sequence range to include in the logo" />
+            </when>
+        </conditional>
+        <param name="size" type="select" label="Output weblogo size" >
+            <option value="large" selected="True">Large</option>
+            <option value="medium">Medium</option>
+            <option value="small">Small</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="pdf" name="output"  label="${logoname}_output.${outformat}">
+            <change_format>
+                <when input="outformat" value="png_print" format="png" />
+                <when input="outformat" value="png" format="png" />
+                <when input="outformat" value="jpeg" format="jpg" />
+                <when input="outformat" value="eps" format="eps" />
+                <when input="outformat" value="logodata" format="txt" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="rgClustal_testout.fasta" />
+            <param name="logoname" value="Galaxy/Rgenetics weblogo" />
+            <param name="outformat" value="jpeg" />
+            <param name="mode" value="complete" />
+            <param name="size" value="medium" />
+            <param name="colours" value="auto" />
+            <param name="units" value="bits" />
+            <output name="output" file="rgWebLogo3_test.jpg" ftype="jpg" compare="sim_size" delta="10000" />
+        </test>
+        <test>
+            <param name="input" value="rgClustal_testout.fasta" />
+            <param name="logoname" value="Galaxy/Rgenetics weblogo" />
+            <param name="outformat" value="png" />
+            <param name="mode" value="complete" />
+            <param name="size" value="medium" />
+            <param name="colours" value="auto" />
+            <param name="units" value="probability" />
+            <output name="output" file="rgWebLogo3_test2.png" ftype="png" compare="sim_size" delta="10000" />
+        </test>
+    </tests>
+    <help><![CDATA[
 **Note**
 
 This tool uses Weblogo3_ in Galaxy to generate a sequence logo. The input file must be a fasta file in your current history.
@@ -119,8 +117,8 @@
 The Weblogo3 program used by this tool will fail if your fasta sequences are not all EXACTLY the same length. The tool will provide a warning
 and refuse to call the weblogo3 executable if irregular length sequences are detected.
 
-Fasta alignments from the companion ClustalW Galaxy tool will work but many other fasta files may cause this tool to fail - please do not file 
-a Galaxy bug report - this is a feature of the tool and a problem with your source data - not a tool error - please make certain all your fasta 
+Fasta alignments from the companion ClustalW Galaxy tool will work but many other fasta files may cause this tool to fail - please do not file
+a Galaxy bug report - this is a feature of the tool and a problem with your source data - not a tool error - please make certain all your fasta
 sequences are the same length!
 
 ----
@@ -135,8 +133,8 @@
 
 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
 
-  </help>
-
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1101/gr.849004</citation>
+    </citations>
 </tool>
-
-