<tool id="mdanalysis_distance" name="Distance Analysis" version="@VERSION@">
    <description>- time series using MDAnalysis</description>
    <macros>
        <import>macros.xml</import>
    </macros>   
    <expand macro="requirements" />
    <command detect_errors="exit_code">
<![CDATA[
     python '$__tool_directory__/distance.py' 
        --itraj '$trajin' 
        --istr '$strin'
        --itrajext '$trajin.ext'
        --istrext '$strin.ext'
        --isegid1 '$segid1' 
        --iresid1 '$resid1' 
        --iname1 '$name1'
        --isegid2 '$segid2'
        --iresid2 '$resid2' 
        --iname2 '$name2'
        --output '$output'
        --odistance_plot '$distance_plot'
    2>&1
]]></command>
    <inputs>
        <expand macro="analysis_inputs"/>
        <param name="segid1"  type="text" value="PRO" label="Segment ID of atom 1"/>
        <param name="resid1"  type="text" value="212" label="Residue ID of atom 1"/>
        <param name="name1"  type="text" value="OE2" label="Atom name of atom 1"/>
        <param name="segid2"  type="text" value="HET" label="Segment ID of atom 2"/>
        <param name="resid2"  type="text" value="3" label="Residue ID of atom 2"/>
        <param name="name2"  type="text" value="C1" label="Atom name of atom 2"/>
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="Distance Analysis raw data"/>  
        <data format="png" name="distance_plot" label="Distance Analysis Plot"/>
    </outputs>
    <tests>
        <test>
            <expand macro="tests_inputs"/>
            <param name="segid1" value="PRO"/>
            <param name="resid1" value="212"/>
            <param name="name1" value="OE2"/>
            <param name="segid2" value="HET"/>
            <param name="resid2" value="3"/>
            <param name="name2" value="C1"/>
            <output name="output" file="Distance_Analysis_raw_data.tabular" />
        </test>
        <test>
            <expand macro="tests_inputs_gmx"/>
            <param name="segid1" value="SYSTEM"/>
            <param name="resid1" value="212"/>
            <param name="name1" value="OE2"/>
            <param name="segid2" value="SYSTEM"/>
            <param name="resid2" value="3"/>
            <param name="name2" value="C1"/>
            <output name="output">
                <assert_contents>
                    <has_n_columns n="2" />
                    <has_line_matching expression="0\s+3.8.*" />
                    <has_line_matching expression="14\s+3.2.*" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**
        
This tool calculates and plots the distance between the two atoms.

_____


.. class:: infomark

**Input**

       - Trajectory file  (DCD).
       - PDB file.
       - Segment IDs, Residue IDs and names of two atoms to calculate distances.

Note that a MDAnalysis 'segment' is a larger organizational unit,  for example one protein or all the solvent molecules or simply the whole system.

_____

        
.. class:: infomark

**Output**

       - Tab-separated file of raw data of distance between two atoms calculated for each frame.
       - Image (as png) of the time series graph.


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