<tool id="mdanalysis_hbonds" name="Hydrogen Bond Analysis" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>- analyze H-bonds between two segments</description>
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>   
    <expand macro="requirements">
        <requirement type="package" version="1.0.5">pandas</requirement>
    </expand>
    <command detect_errors="exit_code">
<![CDATA[
     python '$__tool_directory__/hbonds.py' 
        --itraj '$trajin' 
        --istr '$strin'
        --itrajext '$trajin.ext'
        --istrext '$strin.ext'
        --isegid1 '$segid1'  
        --isegid2 '$segid2'
        --idistance '$distance'
        --iangle '$angle'
        --output '$output'
        --ofreq_output '$freq_output' 
        --onumber_output '$number_output' 
        --otime_output '$time_output'
    2>&1
]]></command>
    <inputs>
        <expand macro="analysis_inputs"/>
        <param name="segid1"  type="text" value="PRO" label="Segment ID of selection 1"/>
        <param name="segid2"  type="text" value="HET" label="Segment ID of selection 2"/>
        <param name="distance" type="float" value="3.0" label="Cutoff distance"/>
        <param name="angle"  type="float" value="120.0" label="Cutoff angle"/>
    </inputs>
    <outputs> 
        <data format="tabular" name="output" label="H-bond analysis raw data"/>
        <data format="tabular" name="freq_output" label="H-bond frequency"/>
        <data format="tabular" name="number_output" label="Number of H-bonds per time step"/>
        <data format="tabular" name="time_output" label="Time steps for each observed H-bond"/>
    </outputs>
    <tests>
        <test>
            <expand macro="tests_inputs"/>
            <param name="distance" value="3.0"/>
            <param name="angle" value="120.0"/>
            <output name="number_output">
              <assert_contents>
                <has_text text="1.000" />
              </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**
        
This tool calculates hydrogen bonds between two segments of the system. 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

**Input**

       - Trajectory file  (DCD).
       - PDB file.
       - Segment IDs of the two segments.
       - Cutoff distance and angle.
     
_____

        
.. class:: infomark

**Output**

       - Tabular files containing H-bond frequency, number of H-bonds Per time step, and time steps for each observed H-bond.


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