comparison solvate.xml @ 15:97b2c06ae168 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3"

14:2c8ed1b52bf7

<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@">1</token>
    </macros>

    <expand macro="requirements" />

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

        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 &>> 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 &>> verbose.txt &&
            mv solv_ions.gro solv.gro
        #end if

    ]]></command>
        <configfiles>

            <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." />

        <expand macro="log" />

    </inputs>
    <outputs>
        <data name="output1" format="gro" from_work_dir="solv.gro"/>
        <data name="output2" format="top" from_work_dir="./top_input.top"/>
        <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">
                <!-- replacement of water with ions is random, thus we cannot 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" file="topol_solv.top" ftype="top" lines_diff="4">
                <assert_contents>
                    <has_line line="SOL         2130" />
                    <has_line line="NA               41" />
                    <has_line line="CL               43" />
                </assert_contents>

15:97b2c06ae168

<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[

        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 &>> 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>

            <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="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>