Mercurial > repos > luis > ball
diff galaxy_stubs/BondOrderAssigner.xml @ 2:605370bc1def draft default tip
Uploaded
author | luis |
---|---|
date | Tue, 12 Jul 2016 12:33:33 -0400 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy_stubs/BondOrderAssigner.xml Tue Jul 12 12:33:33 2016 -0400 @@ -0,0 +1,86 @@ +<?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: [Preparation]--> +<tool id="BondOrderAssigner" name="BondOrderAssigner" version="1.1.0"> + <description>computes bond order assignments for a ligand </description> + <macros> + <token name="@EXECUTABLE@">BondOrderAssigner</token> + <import>macros.xml</import> + </macros> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>BondOrderAssigner + +#if $param_i: + -i $param_i +#end if +#if $param_o: + -o $param_o +#end if +#if $param_max_sol: + -max_sol $param_max_sol +#end if +#if $param_scr_pen: + -scr_pen + #if " " in str($param_scr_pen): + "$param_scr_pen" + #else + $param_scr_pen + #end if +#end if +#if $param_non_opt: + -non_opt $param_non_opt +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_o_id: + -o_id "$adv_opts.param_o_id" +#end if + #if $adv_opts.param_o_dir: + -o_dir "$adv_opts.param_o_dir" +#end if +#end if +</command> + <inputs> + <param name="param_i" type="data" format="mol2" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input mol2-file" help="(-i) "/> + <param name="param_max_sol" type="integer" min="0" max="100" optional="True" value="25" label="maximal number of assignments solutions to compute" help="(-max_sol) "/> + <param name="param_scr_pen" type="select" optional="True" value="Antechamber" label="penalty table (Antechamber, BALL)" help="(-scr_pen) "> + <option value="Antechamber">Antechamber</option> + <option value=" BALL"> BALL</option> + </param> + <param name="param_non_opt" type="integer" min="0" max="1" optional="True" value="0" label="compute sub-optimal assignments as well" help="(-non_opt) "/> + <expand macro="advanced_options"> + <param name="param_o_id" type="text" size="30" value="$o.id" label="output id" help="(-o_id) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_o_dir" type="text" size="30" value="$__new_file_path__" label="output directory for 2nd to last solution" help="(-o_dir) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </expand> + </inputs> + <outputs> + <data name="param_o" format="mol2"/> + </outputs> + <help>This tool computes optimal and sub-optimal bond order assignments based on an atomic penalty function for a given ligand in mol2 file format. + +Optional parameters are the maximal number of solutions to be computed ('-max_sol'), the penalty table specifiying the atomic penalty rules ('-scr_pen'),and a flag indicating if sub-optimal solutions should be computed as well ('-non_opt'). + +Output of this tool is a number of mol2 files each containing one bond order assignment. + +To upload an input file please use the upload tool (Get Data -> Upload File). + +**Further information and help** can be found in our wiki https://github.com/BALL-Project/ball/wiki/BOAConstructor_Help. + +Please cite the following: Dehof, A.K., Rurainski, A., Bui, Q.B.A., Boecker, S., Lenhof, H.-P. & Hildebrandt, A. (2011). Automated Bond Order Assignment as an Optimization Problem. Bioinformatics, 2011 + +</help> +</tool>