changeset 2:aa036496c27a draft

Deleted selected files

--- a/kplogo.xml	Fri Mar 24 16:09:26 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,96 +0,0 @@
-<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>
-
-