diff Codonlogo.xml @ 9:f3462128e87c

Minor alterations to the galaxy interface with some better examples and error messages added.

--- a/Codonlogo.xml	Fri Jan 20 09:03:40 2012 -0500
+++ b/Codonlogo.xml	Mon Jan 30 08:17:57 2012 -0500
@@ -1,6 +1,6 @@
 <tool id="codonlogo" name="Codon Logo" version="3">
   <description>generator for fasta (eg Clustal alignments)</description>
-  <command interpreter="/usr/tmp/bin/python2.7 -W ignore::DeprecationWarning"> 
+  <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 -G $strict --fineprint "$fineprint" --stack-width $stackwidth --stack-height $stackheight --box $box --resolution $resolution --scale-width $scalewidth
 
     #if str($ylabel) != ''
@@ -24,13 +24,13 @@
     -R $compfile 
     #end if
     #if str($comp.mode) == 'Escherichiacoli'
-    -R Escherichiacoli.txt
+    --comp escherichiacoli
     #end if
     #if str($comp.mode) == 'Saccharomycescerevisiae'
-    -R Saccharomycescerevisiae.txt
+    --comp saccharomycescerevisiae
     #end if
     #if str($comp.mode) == 'Homosapiens'
-    -R Homosapiens.txt
+    --comp homosapiens
     #end if
     
     #if $colours.colour == 'part'
@@ -404,13 +404,12 @@
     </conditional>
     <conditional name="comp">
       <param name="mode" type="select" label="Select expected composition: 'equiprobable', 'none' (no small sample correction), or supply a file">
-        
-        <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>
+        <option value="none" >No small sample correction</option>       
+        <option value="equiprobable" >Equiprobable</option>
+        <option value="Homosapiens" >Human</option>
+        <option value="Yeast" >Saccharomycescerevisiae</option>
+        <option value="E.Coli" >Escherichiacoli</option>
+        <option value="From File">from file</option>
         
       </param>
       <when value="auto">