view galaxy_stubs/BindingDBCleaner.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="BindingDBCleaner" name="BindingDBCleaner" version="1.1.0">
  <description>fix bindingdb.org downloads</description>
  <macros>
    <token name="@EXECUTABLE@">BindingDBCleaner</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>BindingDBCleaner

#if $param_i:
  -i $param_i
#end if
#if $param_type:
  -type
  #if " " in str($param_type):
    "$param_type"
  #else
    $param_type
  #end if
#end if
#if $param_o:
  -o $param_o
#end if
#if $param_target:
  -target     "$param_target"
#end if
</command>
  <inputs>
    <param name="param_i" type="data" format="mol2,sdf,drf" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input file" help="(-i) "/>
    <param name="param_type" type="select" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="type of contained activity values: 'Ki' or 'IC50'" help="(-type) ">
      <option value="IC50">IC50</option>
      <option value=" Ki"> Ki</option>
    </param>
    <param name="param_target" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="binding-DB target name" help="(-target) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
  </inputs>
  <expand macro="advanced_options"/>
  <outputs>
    <data name="param_o" metadata_source="param_i" format="input"/>
  </outputs>
  <help>This tool cleans up the sd-properties contained in sd-files downloaded from bindingdb.org.

For all compounds in the input file, the affinity value for the specified target is searched and retained but all other properties are removed. Furthermore, the IC50 or Ki value of each compound is converted to a binding-free-energy value in units of [kJ/mol] that is added as a property-tag named 'binding_free_energy'.

All compounds in the input file for which no IC50 resp. Ki value for the specified target can found, are ignored and not written to the output file.

</help>
</tool>