--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgWebLogo3.xml	Mon Jan 27 09:25:50 2014 -0500
@@ -0,0 +1,141 @@
+<tool id="rgweblogo3" name="Sequence Logo" version="0.4">
+   <description>generator for fasta (eg Clustal alignments)</description>
+   <requirements>
+      <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" size="50" 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="txt">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>
+
+    
+    <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>
+        <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>
+           <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> 
+        </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="txt" 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>
+
+**Note**
+
+This tool uses Weblogo3_ in Galaxy to generate a sequence logo. The input file must be a fasta file in your current history.
+
+It is recommended for (eg) viewing multiple sequence alignments output from the clustalw tool - set the output to fasta and feed
+it in to this tool.
+
+A typical output looks like this
+
+.. image:: ${static_path}/images/rgWebLogo3_test.jpg
+
+----
+
+**Warning about input Fasta format files**
+
+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 
+sequences are the same length!
+
+----
+
+**Attribution**
+
+Weblogo attribution and associated documentation are available at Weblogo3_
+
+This Galaxy wrapper was written by Ross Lazarus for the rgenetics project and the source code is licensed under the LGPL_ like other rgenetics artefacts
+
+.. _Weblogo3: http://weblogo.berkeley.edu/
+
+.. _LGPL: http://www.gnu.org/copyleft/lesser.html
+
+  </help>
+
+</tool>
+
+