<tool id="gromacs_modify_topology" name="Adding New Topology Information" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.09">
    <description>to a GROMACS topology file</description>
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        #if $str($functionality.what2add) == "mol":
            python3 '$__tool_directory__/gmxtras_add_newmolparam.py'
                --top_file '$functionality.inputtopology'
                --atom_file '$functionality.nonbondparam'
                --mol_file '$functionality.bondparam'
                --out '$newtop'
        #end if

        #if $str($functionality.what2add) == "restraints":
            python3 '$__tool_directory__/gmxtras_add_restraints.py'
                --top_file '$functionality.inputtopology'
                --res_file '$functionality.posres'
                --molecule '$functionality.targetmolecule'
                --out '$newtop'
        #end if

        #if $str($functionality.what2add) == "both":
            python3 '$__tool_directory__/gmxtras_add_restraints.py'
                --top_file '$functionality.inputtopology'
                --res_file '$functionality.posres'
                --molecule '$functionality.targetmolecule'
                --out 'odoylerules'
            &&
            python3 '$__tool_directory__/gmxtras_add_newmolparam.py'
                --top_file 'odoylerules'
                --atom_file '$functionality.nonbondparam'
                --mol_file '$functionality.bondparam'
                --out '$newtop'
        #end if

    ]]></command>
    <inputs>
        
        <conditional name="functionality">
             <param name="what2add" type="select" label="What new information are you adding to your topology file?">
                 <option value="mol">A molecule's parameters</option>
                 <option value="restraints">Position restraint information</option>
                 <option value="both">Both a molecule's topology information and position restrain information</option>
             </param>
             <when value="mol">
                 <param name="inputtopology" type="data" format="top" label="GROMACS Topology file to be modified" help="Topology file with missing information"/>
                 <param name="nonbondparam" type="data" format="txt" label="Atom Types with Nonbonded Parameters" help="Atom types information from grep"/>
                 <param name="bondparam" type="data" format="txt,itp" label="Molecule type information with bonded parameters" help="molecule type information"/>
             </when>
             <when value="restraints">
                 <param name="inputtopology" type="data" format="top" label="GROMACS Topology file to be modified" help="Topology file with missing information"/>
                 <param name="posres" type="data" format="itp" label="Position restraint file" help="Position restraint file created previously"/>
		 <param name="targetmolecule" type="text" label="Target molecule type" help="The molecule type name to which the restraints were applied"/>
             </when>
             <when value="both">
                 <param name="inputtopology" type="data" format="top" label="GROMACS Topology file to be modified" help="Topology file with missing information"/>
                 <param name="nonbondparam" type="data" format="txt" label="Atom Types with Nonbonded Parameters" help="Atom types information from grep"/>
                 <param name="bondparam" type="data" format="txt,itp" label="Molecule type information with bonded parameters" help="molecule type information"/>
                 <param name="posres" type="data" format="itp" label="Position restraint file" help="Position restraint file created previously"/>
                 <param name="targetmolecule" type="text" label="Target molecule type" help="The molecule type name to which the restraints were applied"/>
             </when>

        </conditional>  
    </inputs>
    <outputs>
        <data name="newtop" format="top" label="Modified file with new topology information ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <conditional name="functionality">
                <param name="what2add" value="mol" />
                <param name="inputtopology" value="cid1_GMX.top" />
                <param name="nonbondparam" value="water_nonbondedparams.itp" />
                <param name="bondparam" value="water_bondedparams.itp" />
            </conditional>
            <output name="newtop">
                <assert_contents>
                    <has_text text="HW_tip4pew   1       1.008   0.0000  A   0.00000e+00  0.00000e+00"/>
                    <has_text text="  2   HW_tip4pew  1       SOL       HW1      1       0.52422   1.00800"/>
                </assert_contents>
            </output>
        </test>
        <test>
	    <conditional name="functionality">
            	<param name="what2add" value="restraints" />
            	<param name="inputtopology" value="cid1_GMX.top" />
            	<param name="targetmolecule" value="cid1" />
            	<param name="posres" value="posres_cid1.itp" />
            </conditional>
		<output name="newtop">
                <assert_contents>
                    <has_text text=";  i funct       fcx        fcy        fcz"/>
                    <has_text text="  42    1       1000       1000       1000"/>
                </assert_contents>
            </output>
        </test>
        <test>
 	    <conditional name="functionality">
            	<param name="what2add" value="both" />
            	<param name="inputtopology" value="cid1_GMX.top" />
            	<param name="nonbondparam" value="water_nonbondedparams.itp" />
            	<param name="bondparam" value="water_bondedparams.itp" />
            	<param name="targetmolecule" value="cid1" />
            	<param name="posres" value="posres_cid1.itp" />
            </conditional>
		<output name="newtop">
                <assert_contents>
                    <has_text text="HW_tip4pew   1       1.008   0.0000  A   0.00000e+00  0.00000e+00"/>
                    <has_text text="  2   HW_tip4pew  1       SOL       HW1      1       0.52422   1.00800"/>
                    <has_text text=";  i funct       fcx        fcy        fcz"/>
                    <has_text text="  42    1       1000       1000       1000"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

Tool to modify and add new information to GROMACS topology files. This is particularly useful when working with systems
that were created outside of GROMACS (for example, files created in AMBER or CHARMM and then converted over via acpype).
This tool can also be used to complement the "gmx insert-molecules" tool, which currently only modifies the GROMACS
structure files (gro) and requires further modification of the topology file for the newly populated system to be simulation ready.   

.. class:: infomark

**Input**

1) The system topology file you are modifying, 

2) a position restraint file (posres.itp) and specifying the name of the target molecule type you are restraining, 

3) a molecule's atom types/nonbonded parameters to be inserted under the system's global [ atomtypes ], as well as

4) the corresponding bonded parameters of that particular molecule found under [ moleculetype ].

.. class:: infomark

**Outputs**

The new modified GROMACS topology file.


    ]]></help>
    <expand macro="citations">
        <citation type="doi">doi:10.1186/1756-0500-5-367</citation>
    </expand>
</tool>