annotate galaxy_stubs/BondOrderAssigner.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: [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="&lt;class 'CTDopts.CTDopts._Null'&gt;" 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="$o.id" label="output id" help="(-o_id) ">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param name="param_o_dir" type="text" size="30" value="$__new_file_path__" label="output directory for 2nd to last solution" help="(-o_dir) ">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </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 -&gt; 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. &amp; Hildebrandt, A. (2011). Automated Bond Order Assignment as an Optimization Problem. Bioinformatics, 2011

</help>
</tool>