changeset 0:f6226f8823ce draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kplogo.xml	Thu Mar 23 00:47:36 2017 -0400
@@ -0,0 +1,102 @@
+<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 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 $tab_all;
+   
+    </command>
+  <inputs>
+   <page>
+    <param format="fasta" name="input" type="data" label="Fasta File" />
+    
+    <param name="alphabet" type="select" label="Sequence type: DNA/RNA or Protein" >
+      <option value="dna" selected="True">DNA/RNA</option>
+      <option value="protein">Protein</option>
+      <option value="other">Other (not supported yet)</option>
+    </param>
+    
+    <param name="inputtype" type="select" label="Weighted or Ranked" >
+      <option value="" selected="True">Unweighted (FASTA or Tab-delimited) </option>
+      <option value="-ranked">Ranked (FASTA or Tab-delimited)</option>
+      <option value="-weighted">Weighted (Tab-delimited)</option>
+    </param>
+    
+    <param name="maxk" type="select" label="k-mer length"
+      help="k-mer length">
+      <option value="-max_k 4" selected="True">1,2,3,4</option>
+      <option value="-max_k 3">1,2,3</option>
+      <option value="-max_k 2">1,2</option>
+      <option value="-k 4">4</option>
+      <option value="-k 3">3</option>
+      <option value="-k 2">2</option>
+      <option value="-k 1">1</option>
+    </param>
+    
+    <param name="degenerate" type="select" label="Degenerate residual (DNA/RNA only)">
+      <option value="-gapped" selected="True">ACGTN, i.e. gapped</option>
+      <option value="">None (no degenerate residuals)</option>
+      <option value="-degenerate all">all IUPAC residuals: ACGTRYMKWSBDHVN</option>
+    </param>
+    
+    <param name="startPos" type="integer" value="1"/> 
+
+
+   </page>
+  </inputs>
+  <outputs>
+    <data format="pdf" name="logo_info" label="${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 tool uses Weblogo3_ in Galaxy to generate a sequence logo. The input file must be a fasta file in your current history.
+
+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
+
+----
+
+**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!
+
+----
+
+**Attribution**
+
+Weblogo attribution and associated documentation are available at Weblogo3_
+
+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>
+
+</tool>
+
+