Mercurial > repos > luis > ball
diff galaxy_stubs/RMSDCalculator.xml @ 2:605370bc1def draft default tip
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author | luis |
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date | Tue, 12 Jul 2016 12:33:33 -0400 |
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--- /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="<class 'CTDopts.CTDopts._Null'>" 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="<class 'CTDopts.CTDopts._Null'>" 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>