diff Codonlogo.xml @ 15:981eb8c3a756 default tip

Uploaded

--- a/Codonlogo.xml	Fri Feb 24 11:37:26 2012 -0500
+++ b/Codonlogo.xml	Sat Mar 31 16:07:07 2012 -0400
@@ -1,8 +1,12 @@
 <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 -G $strict --fineprint "$fineprint" --stack-width $stackwidth --stack-height $stackheight --box $box --resolution $resolution --scale-width $scalewidth
-
+    codonlogo -F $outformat -s $size -f $input -o $output -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 $scalewidth
+   
+    #if str($logoname) != ''
+    -t "$logoname"
+    #end if
+    
     #if str($ylabel) != ''
     -x "$xlabel" 
     #end if
@@ -332,7 +336,7 @@
   </command>
   <inputs>
     <page>
-      <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 format="text" name="input" type="data" label="Input file."  help="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="" />
       
@@ -346,7 +350,7 @@
     </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." >
+    <param name="frame" type="select" label="Frame to view the alignment."  help="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">+2</option>
@@ -409,7 +413,7 @@
         <option value="Homosapiens" >Human</option>
         <option value="Saccharomycescerevisiae" >Yeast</option>
         <option value="Escherichiacoli" >E.Coli</option>
-        <option value="From File">from file</option>
+        <option value="file">from file</option>
         
       </param>
       <when value="auto">
@@ -419,12 +423,12 @@
       <when value="none">
       </when>
       <when value="file">    
-        <param format="txt" name="compfile" type="data" label="File containing the expected composition of the sequence. expected: a file with 64 codons followed by their probability. it must have 64 lines and each line must have a codon followed by a space followed by a weigt." />
+        <param format="txt" name="compfile" type="data" label="File containing the expected composition of the sequence. "  help="expected: a file with 64 codons followed by their probability. it must have 64 lines and each line must have a codon followed by a space followed by a weight." />
       </when>
       
     </conditional>
     <conditional name="colours">
-      <param name="colour" type="select" label="Choose colours?(it is not required to set values for all of them. Colors can be specified using CSS2 syntax. e.g. 'red', '#FF0000', etc. )">
+      <param name="colour" type="select" label="Choose colours?"  help="it is not required to set values for all of them. Colors can be specified using CSS2 syntax. e.g. 'red', '#FF0000', etc.">
         <option value="no" selected="true">Default colours</option>
         <option value="part">Set your own.</option>
       </param>