# HG changeset patch
# User xuebing
# Date 1490386166 14400
# Node ID 3c13235a05f544885b5d9e6b6e9cd4fdad6d09f8
# Parent  f6226f8823ce1ad6d5909b77b4c64c38feefbcd8
Uploaded

diff -r f6226f8823ce -r 3c13235a05f5 kplogo.xml
--- a/kplogo.xml	Thu Mar 23 00:47:36 2017 -0400
+++ b/kplogo.xml	Fri Mar 24 16:09:26 2017 -0400
@@ -2,7 +2,7 @@
    <description>for positional k-mer analysis</description>
    <command> 
    
-   kpLogo $input $inputtype -o $output -alphabet $alphabet $maxk -startPos $startPos $degenerate 2> tmp; 
+   kpLogo $input $inputtype -o $output -alphabet $alphabet $maxk -startPos $startPos $degenerate -seq $col_seq -weight $col_weight -region $region_start,$region_end  2> tmp; 
    cp ${output}.most.significant.each.position.pdf $output;
    cp ${output}.pdf $logo_prob;
    cp ${output}.info.pdf $logo_info; 
@@ -13,8 +13,8 @@
     </command>
   <inputs>
    <page>
-    <param format="fasta" name="input" type="data" label="Fasta File" />
-    
+    <param format="text" name="input" type="data" label="Input sequences (FASTA or Tabular)" />
+
     <param name="alphabet" type="select" label="Sequence type: DNA/RNA or Protein" >
       <option value="dna" selected="True">DNA/RNA</option>
       <option value="protein">Protein</option>
@@ -27,6 +27,17 @@
       <option value="-weighted">Weighted (Tab-delimited)</option>
     </param>
     
+        
+    <param name="col_seq" type="integer" value="1" label="For tabular input, sequence is in this column:"  /> 
+    
+    <param name="col_weight" type="integer" value="2" label="For tabular input, weight is in this column:"  /> 
+
+    <param name="region_start" type="integer" value="1" label="Starting from position (0 or negative numbers interpreted as distance from the end):"  /> 
+    
+    <param name="region_end" type="integer" value="0" label="Ending at position (0 or negative numbers interpreted as distance from the end):"  /> 
+
+    
+    
     <param name="maxk" type="select" label="k-mer length"
       help="k-mer length">
       <option value="-max_k 4" selected="True">1,2,3,4</option>
@@ -44,8 +55,9 @@
       <option value="-degenerate all">all IUPAC residuals: ACGTRYMKWSBDHVN</option>
     </param>
     
-    <param name="startPos" type="integer" value="1"/> 
+    <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"/> 
 
    </page>
   </inputs>
@@ -63,37 +75,19 @@
 
 **Note**
 
-This tool uses Weblogo3_ in Galaxy to generate a sequence logo. The input file must be a fasta file in your current history.
+This is a wrapper for the positional k-mer analysis tool kpLogo_, which is also available as a web server and stand-alone command-line tool. Please refer to the manual_ on the web server for help information.
 
-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
+To run kpLogo on local Galaxy instances, one needs to compile and install kpLogo locally. Please refer to the web server for details (click here_). 
 
 ----
 
-**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!
+.. _kpLogo: http://kplogo.wi.mit.edu/
 
-----
-
-**Attribution**
-
-Weblogo attribution and associated documentation are available at Weblogo3_
+.. _manual: http://kplogo.wi.mit.edu/manual.html
+  
+.. _here: http://kplogo.wi.mit.edu/manual.html#install-kpLogo-locally
 
-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>