annotate solvate.xml @ 22:598e0078040b draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 5536c9fbb2f680a5f296db81362099e5a68e0587"

<tool id="gmx_solvate" name="GROMACS solvation and adding ions" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>to structure and topology files</description>
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>

    <expand macro="requirements" />

    <command detect_errors="exit_code"><![CDATA[

        ln -s '$ions' ./ions.mdp &&
        ln -s '$gro_input' ./gro_input.gro &&
        ln -s '$top_input' ./top_input.top &&

        gmx solvate -cp ./gro_input.gro -cs ${water_model}.gro -o solv.gro -p ./top_input.top &>> verbose.txt &&
        gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr @MAXWARN_CMD@ &>> verbose.txt
        #if $neutralise or $conc:  ## else this step would do nothing
            &&
            echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL $neutralise -conc $conc -seed $seed &>> verbose.txt &&
            mv solv_ions.gro solv.gro
        #end if

    ]]></command>
        <configfiles>
            <!-- .mdp file for the gromacs simulation -->
            <configfile name="ions">

; Parameters are not so important here as no simulation is run
integrator  = steep
emtol    = 1000.0
emstep      = 0.01 
nsteps    = 1
nstlist        = 1
cutoff-scheme   = Verlet
ns_type        = grid
coulombtype      = cutoff
rcoulomb      = 1.0
rvdw        = 1.0
pbc            = xyz
            </configfile>
        </configfiles>
    <inputs>
        <param argument="gro_input" type="data" format='gro' label="GRO structure file"/>
        <param argument="top_input" type="data" format='top' label="Topology (TOP) file"/>
        <param name="water_model" type="select"  label="Water model for solvation" help="Note SPC is a generic equilibrated 3-point solvent model and can be used as the solvent configuration for any of SPC, SPC/E, or TIP3P water.">
            <option value="spc216" selected="true">SPC (generic three-point model)</option>
            <option value="tip4p">TIP4P (four-point model)</option>
            <option value="tip5p">TIP5P (five-point model)</option>
        </param>
        <param name="neutralise" label="Add ions to neutralise system?" type="select" help="If system is charged, replace an appropriate number of randomly selected solvent molecules with sodium or chloride ions to neutralise it.">
            <option value="-neutral">Yes, add ions</option>
            <option value="">No</option>
        </param>

        <param argument="conc" type="float" value="0" min="0" max="6" label="Specify salt concentration (sodium chloride) to add, in mol/liter" help="Note existing ions in the system are not taken into account - including those added if the neutralise option is selected. Ions are added by randomly replacing water molecules." />
        <param argument="seed" type="integer" value="1" min="0" label="Random seed for adding ions" help="Select a random seed for replacing solvent with ions. Set to 0 to generate a seed." />

        <expand macro="maxwarn" />
        <expand macro="log" />

    </inputs>
    <outputs>
        <data name="output1" format="gro" from_work_dir="solv.gro" label="GROMACS solvation (GRO) on ${on_string}"/>
        <data name="output2" format="top" from_work_dir="./top_input.top" label="GROMACS solvation (TOP) on ${on_string}"/>
        <expand macro="log_outputs" />
    </outputs>
    <tests>
        <test>
            <param name="gro_input" value="newbox.gro" />
            <param name="neutralise" value="-neutral" />
            <param name="top_input" value="topol.top" />
            <param name="water_model" value="spc216" />
            <param name="conc" value="1" />
            <output name="output1" ftype="gro">
                <!-- file is big, thus we do not compare the whole file -->
                <assert_contents>
                    <has_text text="1.671   1.591   3.533"/>
                    <has_text text="2.032   2.417   1.345"/>
                    <has_text text="3.438   1.662   0.307"/>
                    <has_text text="2218CL"/>
                    <has_text text="2147NA"/>
                </assert_contents>
            </output>
            <output name="output2" ftype="top">
                <assert_contents>
                    <has_line line="SOL         2130" />
                    <has_line line="NA               41" />
                    <has_line line="CL               43" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="gro_input" value="newbox.gro" />
            <param name="neutralise" value="" />
            <param name="top_input" value="topol.top"/>
            <param name="water_model" value="spc216" />
            <param name="conc" value="0" />
            <output name="output1" ftype="gro">
                <assert_contents>
                    <has_text text="1.671   1.591   3.533"/>
                    <has_text text="2.032   2.417   1.345"/>
                    <has_text text="3.438   1.662   0.307"/>
                    <not_has_text text="2218CL"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

This tool solvates a system prior to a GROMACS simulation. In addition, sodium or chloride ions can be added if necessary to ensure the system is charge-neutral.

_____

.. class:: infomark

**Input**

       - GRO structure file.
       - Topology (TOP) file.

In addition, a water model must be selected - this should be consistent with the one selected previously in the system setup.

_____

        
.. class:: infomark

**Output**

       - GRO structure file.

    ]]></help>

    <expand macro="citations" />
</tool>