diff galaxy_stubs/SimilarityAnalyzer.xml @ 2:605370bc1def draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_stubs/SimilarityAnalyzer.xml	Tue Jul 12 12:33:33 2016 -0400
@@ -0,0 +1,55 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
+<!--Proposed Tool Section: [Analysis]-->
+<tool id="SimilarityAnalyzer" name="SimilarityAnalyzer" version="0.9">
+  <description>analyze similarity between molecule files</description>
+  <macros>
+    <token name="@EXECUTABLE@">SimilarityAnalyzer</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>SimilarityAnalyzer
+
+#if $param_i1:
+  -i1 $param_i1
+#end if
+#if $param_i2:
+  -i2 $param_i2
+#end if
+#if $param_o:
+  -o $param_o
+#end if
+#if $param_title:
+  -title     "$param_title"
+#end if
+#if $param_quiet:
+  -quiet $param_quiet
+#end if
+</command>
+  <inputs>
+    <param name="param_i1" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input molecule file 1" help="(-i1) "/>
+    <param name="param_i2" type="data" format="xyz.gz,ac,drf.gz,mol2.gz,mol2,sdf.gz,pdb.gz,ent.gz,mol.gz,hin.gz,sdf,ent,brk.gz,mol,ac.gz,brk,xyz,pdb,hin,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input molecule file 2" help="(-i2) "/>
+    <param name="param_title" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="plot title" help="(-title) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_quiet" type="integer" min="0" max="1" optional="True" value="0" label="by quiet, i.e. do not print status" help="(-quiet) "/>
+  </inputs>
+  <expand macro="advanced_options"/>
+  <outputs>
+    <data name="param_o" format="pdf"/>
+  </outputs>
+  <help>This tool evaluates the similarity between molecules in two input files and creates a distribution plot to visualize the result.
+
+Therefore, for each molecule a pathway-based, hashed binary fingerprint is generated and compared to the fingerprint of other molecules by use of the Tanimoto similarity measure.
+The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable.
+
+The resulting plot (in form of an eps-, png- or pdf-file; as chosen) shows the distribution of similarity values obtained by comparing each molecule in input file 1 against each molecule in input file 2.
+
+</help>
+</tool>