annotate parmconv.xml @ 8:30120022aa5c draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f6acbf6f5875904c5b0c69445da0bf44932611c6"

<tool id="parmconv" name="Convert Parameters" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
  <description>to AMBER prmtop in preparation for MMGBSA/MMPBSA</description>
  <macros>
    <import>macros.xml</import>
    <token name="@GALAXY_VERSION@">0</token>
  </macros>
  <expand macro="requirements">
    <requirement type="package" version="3.4.3">parmed</requirement>
    <requirement type="package" version="2021.3">gromacs</requirement>
    <requirement type="package" version="3.0.1">jinja2</requirement>
  </expand>
  <command detect_errors="exit_code">
    <![CDATA[
    #if $param_inputs.fmt == "GROMACS":
      python '$__tool_directory__/parmconv.py'
        --istr '$param_inputs.str_in'
        --itop '$param_inputs.top_in'
        $param_inputs.modbehaviour.removedihe
        $param_inputs.modbehaviour.removebox
        --iradii '$param_inputs.modbehaviour.radii'
        --istripmask '$stripmask_ligand'
        --o_prmtop '$prmtop_ligand'
      2>&1  &&
      python '$__tool_directory__/parmconv.py'
        --istr '$param_inputs.str_in'
        --itop '$param_inputs.top_in'
        $param_inputs.modbehaviour.removedihe
        $param_inputs.modbehaviour.removebox
        --iradii '$param_inputs.modbehaviour.radii'
        --istripmask '$stripmask_receptor'
        --o_prmtop '$prmtop_receptor'
      2>&1 &&
      python '$__tool_directory__/parmconv.py'
        --istr '$param_inputs.str_in'
        --itop '$param_inputs.top_in'
        $param_inputs.modbehaviour.removedihe
        $param_inputs.modbehaviour.removebox
        --iradii '$param_inputs.modbehaviour.radii'
        --istripmask '$stripmask_complex'
        --o_prmtop '$prmtop_complex'
      2>&1 &&
      python '$__tool_directory__/parmconv.py'
        --istr '$param_inputs.str_in'
        --itop '$param_inputs.top_in'
        $param_inputs.modbehaviour.removedihe
        $param_inputs.modbehaviour.removebox
        --iradii '$param_inputs.modbehaviour.radii'
        --istripmask '$stripmask_solvatedcomplex'
        --o_prmtop '$prmtop_solvatedcomplex'
      2>&1
    #else
      python '$templating_script' '$inputs' &&
      PATH_TO_PARMED=\$(dirname `which parmed`) &&
      export AMBERHOME=\$(dirname \$PATH_TO_PARMED) &&
      export GMXDATA=\$AMBERHOME/share/gromacs/top/ &&
      parmed -i ligand.script -O &&
      parmed -i receptor.script -O &&
      parmed -i complex.script -O &&
      parmed -i solvatedcomplex.script -O
    #end if
      ]]>
  </command>
  <configfiles>
    <inputs name="inputs"/>
    <configfile name="templating_script">
      <![CDATA[

import os
import sys
import json

from jinja2 import Environment, FileSystemLoader
input_json_path = sys.argv[1]
params = json.load(open(input_json_path, "r"))
currentpath = "$__tool_directory__"  # should work generally
template_environment = Environment(loader=FileSystemLoader(currentpath),lstrip_blocks=True, trim_blocks=True)
template = template_environment.get_template('template_parmconv.j2')
params['fmt'] = '$param_inputs.fmt'
#if str($param_inputs.fmt)  == 'AMBER':
params["top_in"] = '$param_inputs.top_in'
#else:
params["top_in"] = '$param_inputs.top_in'
params["str_in"] = '$param_inputs.str_in'
#end if
params['prmtop_ligand'] =   '$prmtop_ligand'
params['prmtop_receptor'] =  '$prmtop_receptor'
params['prmtop_complex'] =   '$prmtop_complex'
params['prmtop_solvatedcomplex'] = '$prmtop_solvatedcomplex'
print(params)


def unescape(cond_text):
    """
    # Unescape if input has been escaped - credit @bgruening //github.com/bgruening/galaxytools.git get_online_data.py
    """
    mapped_chars = { '>' :'__gt__',
                 '<' :'__lt__',
                 "'" :'__sq__',
                 '"' :'__dq__',
                 '[' :'__ob__',
                 ']' :'__cb__',
                 '{' :'__oc__',
                 '}' :'__cc__',
                 '@' : '__at__',
                 '\n' : '__cn__',
                 '\r' : '__cr__',
                 '\t' : '__tc__',
                 '&' : '__and__'
                 }
    for key, value in mapped_chars.items():
        cond_text = cond_text.replace( value, key )
    return cond_text

def run_template(params=params, system="ligand"):
    """
    # Render template on a selected system using a local parameter copy
    """
    localparams=params.copy() # shallow copy ok for simple variables
    localparams['stripmask']=unescape(localparams['stripmask_'+system])
    localparams['prmtop_out']=localparams['prmtop_'+system]
    print(localparams)
    with open(system+'.script','w+') as f:
        f.write(template.render(localparams))

systems = ['ligand', 'receptor', 'complex', 'solvatedcomplex']
for system in systems:
    run_template(system=system)

]]>
    </configfile>
  </configfiles>
  <inputs>
    <conditional name="param_inputs">
      <param name="fmt" type="select" label="Input format">
        <option selected="True" value="AMBER">AMBER</option>
        <option value="GROMACS">GROMACS</option>
      </param>
      <when value="AMBER">
        <param name="top_in" type="data" label="Input topology (prmtop) file" format="txt"/>
      </when>
      <when value="GROMACS">
        <param name="top_in" type="data" label="Input topology (top) file" format="top"/>
        <param name="str_in" type="data" label="Input structure (gro) file" format="gro"/>
        <section name="modbehaviour" title="Modify behaviour" expanded="false">
          <param name="removedihe" type="boolean" truevalue="--removedihe" falsevalue="" checked="false" label="Remove all zero period dihedrals" help="This will remove zero period dihedrals from the generated topology"/>
          <param name="removebox" type="boolean" truevalue="--removebox" falsevalue="" checked="false" label="Remove periodic box information" help="This will remove periodic information from the generated topology"/>
          <param name="radii" type="select"  label="Radii to use" help="Select the radii to use. Default is mbondi.">
              <option selected="True" value="mbondi">mbondi</option>
              <option value="mbondi2">mbondi2</option>
              <option value="mbondi3">mbondi3</option>
              <option value="bondi">bondi</option>
              <option value="amber6">amber6</option>
          </param>
        </section>
      </when>
    </conditional>
    <param name="stripmask_ligand" type="text" label="Ligand selection" value="!:UNL" help="Define a valid AMBER stripmask that will select only the ligand">
      <sanitizer>
        <valid initial="string.printable">
          <add value="&amp;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="stripmask_receptor" type="text" label="Receptor selection" value=":NA,SOL,UNL" help="Define a valid AMBER stripmask that will select only the receptor">
      <sanitizer>
        <valid initial="string.printable">
          <add value="&amp;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="stripmask_complex" type="text" label="Complex selection" value=":NA,SOL" help="Define a valid AMBER stripmask that will select the complex (receptor with ligand)">
      <sanitizer>
        <valid initial="string.printable">
          <add value="&amp;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="stripmask_solvatedcomplex" type="text" label="Solvated complex selection" help="Define a valid AMBER stripmask that will select the solvated complex (includes water and ions)">
      <sanitizer>
        <valid initial="string.printable">
          <add value="&amp;"/>
        </valid>
      </sanitizer>
    </param>
  </inputs>
  <outputs>
    <data format="txt" name="prmtop_ligand" label="ligand prmtop"/>
    <data format="txt" name="prmtop_receptor" label="receptor prmtop"/>
    <data format="txt" name="prmtop_complex" label="complex prmtop"/>
    <data format="txt" name="prmtop_solvatedcomplex" label="solvated complex prmtop"/>
  </outputs>
  <tests>
    <test>
      <!--example in this test is not solvated but sufficient -->
      <param name="fmt" value="AMBER"/>
      <conditional name="param_inputs">
        <param name="top_in" value="complex.prmtop"/>
      </conditional>
      <param name="stripmask_ligand" value="!:RAL"/>
      <param name="stripmask_receptor" value=":NA,CL,SOL,WAT,RAL"/>
      <param name="stripmask_complex" value=":NA,CL,SOL,WAT"/>
      <output name="prmtop_ligand">
        <assert_contents>
          <has_text text="      61      15"/>
          <has_text text="%FLAG MASS"/>
          <has_text text="RAL"/>
        </assert_contents>
      </output>
      <output name="prmtop_receptor">
        <assert_contents>
          <has_text text="    3880      15"/>
          <has_text text="%FLAG MASS"/>
          <has_text text="ALA LEU"/>
          <not_has_text text="RAL "/>
        </assert_contents>
      </output>
      <output name="prmtop_complex">
        <assert_contents>
          <has_text text="    3941      15"/>
          <has_text text="%FLAG MASS"/>
          <has_text text="ALA LEU"/>
          <has_text text="RAL"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <!--example in this test is from @sbrays' gromacs tests. It has no ligand but is sufficient and will not take extra space in the repo! -->
      <param name="fmt" value="GROMACS"/>
      <conditional name="param_inputs">
        <param name="top_in" value="topol_solv.top"/>
        <param name="str_in" value="solv_ions.gro"/>
      </conditional>
      <!-- pretending CL is a ligand -->
      <param name="stripmask_ligand" value="!:CL"/>
      <param name="stripmask_receptor" value=":NA,CL,SOL,WAT"/>
      <!-- test a fairly complex selection. All backbone oxygens in residues 1-500 but not in water, lysine or arginine -->
      <param name="stripmask_solvatedcomplex" value=":1-500@O&amp;!(:WAT|:LYS,ARG)"/>
      <output name="prmtop_ligand">
        <assert_contents>
          <has_text text="%FLAG MASS"/>
          <has_text text="CL"/>
          <has_text text="SOLVENT_POINTERS"/>
          <has_text text="BOX_DIMENSIONS"/>
        </assert_contents>
      </output>
      <output name="prmtop_receptor">
        <assert_contents>
          <has_text text="%FLAG MASS"/>
          <has_text text="LYS VAL PHE "/>
          <has_text text="SOLVENT_POINTERS"/>
          <has_text text="BOX_DIMENSIONS"/>
          <not_has_text text="CL "/>
        </assert_contents>
      </output>
      <output name="prmtop_solvatedcomplex">
        <assert_contents>
          <has_text text="%FLAG MASS"/>
          <has_text text="LYS VAL PHE"/>
          <has_text text="SOLVENT_POINTERS"/>
          <has_text text="BOX_DIMENSIONS"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <!-- test with removing dihedrals and periodicity -->
      <param name="fmt" value="GROMACS"/>
      <conditional name="param_inputs">
        <param name="top_in" value="topol_solv.top"/>
        <param name="str_in" value="solv_ions.gro"/>
      </conditional>
      <!-- dihedrals and periodicity -->
      <param name="removedihe" value="--removedihe"/>
      <param name="removebox" value="--removebox"/>
      <!-- pretending CL is a ligand -->
      <param name="stripmask_ligand" value="!:CL"/>
      <param name="stripmask_receptor" value=":NA,CL,SOL,WAT"/>
      <!-- test a fairly complex selection. All backbone oxygens in residues 1-500 but not in water, lysine or arginine -->
      <param name="stripmask_solvatedcomplex" value=":1-500@O&amp;!(:WAT|:LYS,ARG)"/>
      <output name="prmtop_ligand">
        <assert_contents>
          <has_text text="%FLAG MASS"/>
          <has_text text="CL"/>
          <not_has_text text="SOLVENT_POINTERS"/>
          <not_has_text text="BOX_DIMENSIONS"/>
        </assert_contents>
      </output>
      <output name="prmtop_receptor">
        <assert_contents>
          <has_text text="%FLAG MASS"/>
          <has_text text="LYS VAL PHE "/>
          <not_has_text text="CL "/>
          <not_has_text text="SOLVENT_POINTERS"/>
          <not_has_text text="BOX_DIMENSIONS"/>
        </assert_contents>
      </output>
      <output name="prmtop_solvatedcomplex">
        <assert_contents>
          <has_text text="%FLAG MASS"/>
          <has_text text="LYS VAL PHE"/>
          <not_has_text text="SOLVENT_POINTERS"/>
          <not_has_text text="BOX_DIMENSIONS"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help>
    <![CDATA[
    .. class:: infomark

    **What it does**

    This tool converts parameter and topology files that represent a solvated complex into parameter files for the ligand, receptor, complex and solvated complex in AMBER prmtop format. These files are needed for MMGBSA/MMPBSA calculations.

    .. class:: infomark

    **How it works**

    AmberTools' ParmEd is used to strip unneeded atoms and save the parameter files. The stripmasks are defined by the user.

    .. class:: infomark

    **Outputs created**

    prmtop files for the ligand, receptor, complex and solvated complex.

    .. class:: infomark

    **User guide and documentation**

    - The `AmberTools Manual`_
    - The `Parmed Documentation`_


    .. _`AmberTools Manual`: https://ambermd.org/doc12/Amber18.pdf
    .. _`Parmed Documentation`: https://parmed.github.io/ParmEd/html/index.html


    ]]>
  </help>
  <expand macro="citations">
    <citation type="bibtex">@misc{parmed_2020, author = {ParmEd}, title = {ParmEd/ParmEd}, url={https://github.com/ParmEd/ParmEd}, abstract = {Parameter/topology editor and molecular simulator. Contribute to ParmEd/ParmEd development by creating an
      account on GitHub.}, urldate = {2020-04-03}, publisher = {GitHub}, year = {2020}, month = mar, }</citation>
  </expand>
</tool>