annotate galaxy_stubs/PDBCutter.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="PDBCutter" name="PDBCutter" version="1.1.0">
  <description>separate ligand and receptor  </description>
  <macros>
    <token name="@EXECUTABLE@">PDBCutter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>PDBCutter

#if $param_i:
  -i $param_i
#end if
#if $param_rec:
  -rec $param_rec
#end if
#if $param_lig:
  -lig $param_lig
#end if
#if $param_lig_chain:
  -lig_chain     "$param_lig_chain"
#end if
#if $param_lig_name:
  -lig_name     "$param_lig_name"
#end if

#if $rep_param_rm_ch:
-rm_ch
  #for token in $rep_param_rm_ch:
    #if " " in str(token):
      "$token.param_rm_ch"
    #else
      $token.param_rm_ch
    #end if
  #end for
#end if

#if $rep_param_rm_res:
-rm_res
  #for token in $rep_param_rm_res:
    #if " " in str(token):
      "$token.param_rm_res"
    #else
      $token.param_rm_res
    #end if
  #end for
#end if
</command>
  <inputs>
    <param name="param_i" type="data" format="pdb" optional="False" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="input pdb-file" help="(-i) "/>
    <param name="param_lig_chain" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="chain-name of ligand" help="(-lig_chain) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_lig_name" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="ligand name" help="(-lig_name) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <repeat name="rep_param_rm_ch" min="0" max="1" title="param_rm_ch">
      <param name="param_rm_ch" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="protein chains that are to be deleted" help="(-rm_ch) ">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <repeat name="rep_param_rm_res" min="0" max="1" title="param_rm_res">
      <param name="param_rm_res" type="text" size="30" value="&lt;class 'CTDopts.CTDopts._Null'&gt;" label="pdb-residues that are to be deleted (" help="(-rm_res) e.g. water or ions)">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
  </inputs>
  <expand macro="advanced_options"/>
  <outputs>
    <data name="param_rec" format="pdb"/>
    <data name="param_lig" format="pdb"/>
  </outputs>
  <help>This tool splits a given pdb-file into two files containing receptor and reference ligand, respectively.

The name of the reference ligand (exactly as it appears in the pdb-file) and the name of its chain need to be specified by '-lig_name' and '-lig_chain'.
Optionally, chains (e.g. in case of multimers) or pdb-residues (e.g. water or ions) that you don't need can be deleted from the receptor. In this case, specify their names with '-rm_ch' or '-rm_res'.

Output of this tool is one pdb-file containing the receptor-structure, i.e. the protein w/o reference ligand and w/o undesired chains/residues (if any were specified), and one pdb-file containing the reference ligand.

</help>
</tool>