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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy_stubs/RMSDCalculator.xml	Tue Jul 12 12:33:33 2016 -0400
@@ -0,0 +1,44 @@
+<?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="RMSDCalculator" name="RMSDCalculator" version="1.1.0">
+  <description>calculate RMSD between ligand poses</description>
+  <macros>
+    <token name="@EXECUTABLE@">RMSDCalculator</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>RMSDCalculator
+
+#if $param_i:
+  -i $param_i
+#end if
+#if $param_org:
+  -org $param_org
+#end if
+#if $param_o:
+  -o $param_o
+#end if
+#if $param_quiet:
+  -quiet $param_quiet
+#end if
+</command>
+  <inputs>
+    <param name="param_i" 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" help="(-i) "/>
+    <param name="param_org" 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="molecule file containing the original ('true') poses" help="(-org) "/>
+    <param name="param_quiet" type="integer" min="0" max="1" optional="True" value="0" label="by quiet, i.e. do not print progress information" help="(-quiet) "/>
+  </inputs>
+  <expand macro="advanced_options"/>
+  <outputs>
+    <data name="param_o" format="mol2"/>
+  </outputs>
+  <help>This tool calculates the RMSD between different conformations of the same molecule.
+
+This tool can be used to evaluate the differences between ligand poses taken from co-crystal structures, e.g. generated by a docking run.
+Note:Molecules may be sorted differently in the two input files; a topology hashkey will be used to match molecules to each other.
+
+Output of this tool is a molecule file which will for each molecule contain a property-tag 'RMSD' holding the calculated RMSD value.
+
+</help>
+</tool>