# HG changeset patch
# User xuebing
# Date 1490386196 14400
# Node ID 7c3170671f1b618e502f370caed41c217cb98213
# Parent  aa036496c27a9084a078b4f0903394a2c848791c
Uploaded

diff -r aa036496c27a -r 7c3170671f1b kplogo.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kplogo.xml	Fri Mar 24 16:09:56 2017 -0400
@@ -0,0 +1,96 @@
+<tool id="kplogo" name="kpLogo" version="1.0">
+   <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; 
+   cp ${output}.most.significant.each.position.pdf $output;
+   cp ${output}.pdf $logo_prob;
+   cp ${output}.info.pdf $logo_info; 
+   cp ${output}.freq.pdf $logo_freq;
+   cp ${output}.most.significant.each.position.txt $tab_most;
+   cp ${output}.pass.p.cutoff.txt $tab_all;
+   
+    </command>
+  <inputs>
+   <page>
+    <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>
+      <option value="other">Other (not supported yet)</option>
+    </param>
+    
+    <param name="inputtype" type="select" label="Weighted or Ranked" >
+      <option value="" selected="True">Unweighted (FASTA or Tab-delimited) </option>
+      <option value="-ranked">Ranked (FASTA or Tab-delimited)</option>
+      <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>
+      <option value="-max_k 3">1,2,3</option>
+      <option value="-max_k 2">1,2</option>
+      <option value="-k 4">4</option>
+      <option value="-k 3">3</option>
+      <option value="-k 2">2</option>
+      <option value="-k 1">1</option>
+    </param>
+    
+    <param name="degenerate" type="select" label="Degenerate residual (DNA/RNA only)">
+      <option value="-gapped" selected="True">ACGTN, i.e. gapped</option>
+      <option value="">None (no degenerate residuals)</option>
+      <option value="-degenerate all">all IUPAC residuals: ACGTRYMKWSBDHVN</option>
+    </param>
+    
+    <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>
+  <outputs>
+    <data format="pdf" name="logo_info" label="${tool.name} on ${on_string}: info"/>
+    <data format="pdf" name="logo_freq" label="${tool.name} on ${on_string}: freq"/>
+    <data format="pdf" name="logo_prob" label="${tool.name} on ${on_string}: prob"/>
+    <data format="pdf" name="output" label="${tool.name} on ${on_string}: kmer"/>
+    <data format="tabular" name="tab_all" label="${tool.name} on ${on_string}: all_kmer"/>
+    <data format="tabular" name="tab_most" label="${tool.name} on ${on_string}: most_sig"/>
+
+
+  </outputs>
+  <help>
+
+**Note**
+
+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.
+
+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_). 
+
+----
+
+
+.. _kpLogo: http://kplogo.wi.mit.edu/
+
+.. _manual: http://kplogo.wi.mit.edu/manual.html
+  
+.. _here: http://kplogo.wi.mit.edu/manual.html#install-kpLogo-locally
+
+
+  </help>
+
+</tool>
+
+