# HG changeset patch
# User xuebing
# Date 1490388563 14400
# Node ID 00b951fec5f7a23607aa3de5409ccb951d02c687
# Parent  7c3170671f1b618e502f370caed41c217cb98213
Uploaded

diff -r 7c3170671f1b -r 00b951fec5f7 kplogo.xml
--- a/kplogo.xml	Fri Mar 24 16:09:56 2017 -0400
+++ b/kplogo.xml	Fri Mar 24 16:49:23 2017 -0400
@@ -2,7 +2,13 @@
    <description>for positional k-mer analysis</description>
    <command> 
    
-   kpLogo $input $inputtype -o $output -alphabet $alphabet $maxk -startPos $startPos $degenerate -seq $col_seq -weight $col_weight -region $region_start,$region_end  2> tmp; 
+   kpLogo $input $inputtype -o $output -alphabet $alphabet $maxk -startPos $startPos $degenerate -seq $col_seq -weight $col_weight -region $region_start,$region_end     
+   #if $background.background_model == '-bg'
+-bgfile $background_input
+#else
+$background.background_model
+#end if 
+  2> tmp; 
    cp ${output}.most.significant.each.position.pdf $output;
    cp ${output}.pdf $logo_prob;
    cp ${output}.info.pdf $logo_info; 
@@ -55,6 +61,22 @@
       <option value="-degenerate all">all IUPAC residuals: ACGTRYMKWSBDHVN</option>
     </param>
     
+
+ 
+  <conditional name="background">
+    <param name="background_model" type="select" label="Background model (only for unweighted sequences)">
+      <option value="" selected="True">Average across all positions in input sequences</option>
+      <option value="-shuffle 100,2">Shuffle each input sequence 100 times preserving di-residual frequency</option>
+      <option value="-markov 1">Markov model learned from input sequences, first order</option>
+      <option value="-bg">Background sequences (not supported yet in Galaxy)</option>
+    </param>
+        <when value="-bg">    
+               <param format="text" name="background_input" type="data" label="Background sequences (FASTA or Tabular)" />
+        </when>
+  </conditional>
+   
+
+    
     <param name="startPos" type="integer" value="1" label="Redefine position 1. The positions before it will be numbered as -1, -2, etc (no 0)." /> 
 
     <param name="fix" type="float" value="0.75" label="Fixation frequency"/>