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

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<?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>