<tool id="gmx_rmsf" name="GROMACS RMSF calculation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="21.09">
    <description>of molecular structures</description>
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[

        ln -s '$traj_input' ./traj_input.${traj_input.ext} &&
        ln -s '$structure_input' ./structure_input.${structure_input.ext} &&
        #if $ndx_input:
            ln -s '$ndx_input' ./ndx_input.${ndx_input.ext} &&
        #end if
        echo '$index' | gmx rmsf

        ##inputs
        -f ./traj_input.${traj_input.ext}
        -s ./structure_input.${structure_input.ext}
        #if $ndx_input:
            -n ./ndx_input.${ndx_input.ext}
        #end if
        -xvg '$outputformat'

        ## other options
        #if $resavg == 'true':
            -res
        #end if

        >> verbose.txt 2>&1
 
    ]]></command>
    <inputs>
        <param name="traj_input" type="data" format="trr,xtc" label="Trajectory file" help="In XTC or TRR format"/>
        <param name="structure_input" type="data" format="tpr,pdb,gro" label="Structure file" help="In TPR, PDB, or GRO format. Use a tpr file if your system contains nonstandard atom types, as atomic masses may not be directly obtained from PDB or GRO files."/>
        <param name="ndx_input" type="data" format="ndx" optional="true" label="Index (NDX) file" help="Index file (optional) containing your system's different atomic and molecular groups. If not specified, GROMACS uses a default set of groups."/>
        <param name="index" type="integer" value="0" min="0" label="Index of group" help="Index of group for calculating the Root Mean Square Fluctuation (RMSF) - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0)."/>
        <param name="resavg" type="select" label="Calculate average RMSF for entire residues?" help="This option works best if the selected index group mainly includes whole residues.">
            <option value="false">No</option>
            <option value="true">Yes</option>
        </param>
        <param name="outputformat" type="select" label="Output format" help="The default XVG format is compatible with XMGRACE and includes all of the graph's parameters. The raw data just includes 2 columns, one for the frame index and second for the corresponding RMSF value.">
            <option value="xmgrace" selected="true">XVG</option>
            <option value="none">Raw Data</option>
        </param>
        <expand macro="log"/>
    </inputs>
    <outputs>
        <data name="rmsf_output" format="xvg" from_work_dir="rmsf.xvg" label="GROMACS calculation of RMSF on ${on_string}"/>
        <expand macro="log_outputs"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="traj_input" value="npt.xtc"/>
            <param name="structure_input" value="npt.tpr" ftype="tpr"/>
            <param name="ndx_input" value="index.ndx" ftype="ndx"/>
            <param name="index" value="3"/>
            <param name="outputformat" value="xmgrace"/>
            <output name="rmsf_output" ftype="xvg">
                <assert_contents>
                    <has_text text="5   0.0113"/>
                    <has_text text="27   0.0136"/>
                    <has_text text="43   0.0134"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="traj_input" value="npt.xtc"/>
            <param name="structure_input" value="npt.tpr" ftype="tpr"/>
            <param name="ndx_input" value="index.ndx" ftype="ndx"/>
            <param name="index" value="1"/>
            <param name="resavg" value="true"/>
            <param name="outputformat" value="none"/>
            <output name="rmsf_output" ftype="xvg">
                <assert_contents>
                    <has_text text="1   0.0263"/>
                    <has_text text="2   0.0230"/>
                    <has_text text="3   0.0201"/>
                </assert_contents>
            </output>
        </test>
        <!-- test without optional ndx -->
        <test expect_num_outputs="1">
            <param name="traj_input" value="npt.xtc"/>
            <param name="structure_input" value="npt.tpr" ftype="tpr"/>
            <param name="index" value="1"/>
            <param name="resavg" value="true"/>
            <param name="outputformat" value="none"/>
            <output name="rmsf_output" ftype="xvg">
                <assert_contents>
                    <has_text text="1   0.0263"/>
                    <has_text text="2   0.0230"/>
                    <has_text text="3   0.0201"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

        .. class:: infomark
        
        **What it does**
        
        This tool calculates a structure's Root Mean Square Fluctuation (RMSF), using GROMACS.
        
_____
        
        .. class:: infomark
        
        **Input**
        
               - GRO, PDB, or TPR structure file.
               - TRR or XTC trajectory file.
        
        
_____
        
        
        .. class:: infomark
        
        **Output**
        
               - XVG file containing RMSF results.
        
            ]]></help>
    <expand macro="citations"/>
</tool>