<?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: [Convert, combine and store]-->
<tool id="PoseIndices2PDB" name="PoseIndices2PDB" version="1.1.0">
  <description>converts pose indices into PDB files </description>
  <macros>
    <token name="@EXECUTABLE@">PoseIndices2PDB</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>PoseIndices2PDB

#if $param_i_clust:
  -i_clust $param_i_clust
#end if
#if $param_i_trans:
  -i_trans $param_i_trans
#end if
#if $param_i_pdb:
  -i_pdb $param_i_pdb
#end if
#if $param_o:
  -o $param_o
#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_clust" type="data" format="txt" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input cluster index file" help="(-i_clust) "/>
    <param name="param_i_trans" type="data" format="dcd" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input tranformation file" help="(-i_trans) "/>
    <param name="param_i_pdb" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input reference pdb file" help="(-i_pdb) "/>
    <expand macro="advanced_options">
      <param name="param_o_id" type="text" size="30" value="$o.id" label="output file name prefix for 2nd to last pdb file" help="(-o_id) ">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <param name="param_o_dir" type="text" size="30" value="$__new_file_path__" label="output directory for 2nd to last pdb file" help="(-o_dir) ">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </expand>
  </inputs>
  <outputs>
    <data name="param_o" format="pdb"/>
  </outputs>
  <help>This tool converts all pose indices from a given transformation file and the corresponding reference PDBFile into separate PDBFiles.

Parameters are the input pose index file (-i_clust), the original transformation file (-i_trans), the corresponding reference pdb file (-i_pdb) and a naming schema for the resulting pdb files (-o). 

Output of this tool is a set of PDBFiles representing the docking poses belonging to the given input cluster.

</help>
</tool>