Mercurial > repos > davidmurphy > codonlogo

diff Codonlogo.xml @ 9:f3462128e87c

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Minor alterations to the galaxy interface with some better examples and error messages added.
author davidmurphy
date Mon, 30 Jan 2012 08:17:57 -0500
parents 5149eb3a89c2
children 20716450be87
line wrap: on
line diff
--- 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">