annotate hbonds.xml @ 0:469ad3ea5a5f draft

planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1

<tool id="mdanalysis_hbonds" name="Hydrogen Bond Analysis" version="@VERSION@">
    <description>Analyze hbonds between two segments</description>
    <macros>
        <import>macros.xml</import>
    </macros>   
    <expand macro="requirements">
        <requirement type="package" version="0.24.2">pandas</requirement>
    </expand>
    <command detect_errors="exit_code">
<![CDATA[
     python '$__tool_directory__/hbonds.py' 
        --idcd '$dcdin' 
        --ipdb '$pdbin'
        --isegid1 '$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="Segid of selection 1"/>
        <param name="segid2"  type="text" value="HET" label="Segid 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="Hbond Analysis raw data"/>
        <data format="tabular" name="freq_output" label="Hbond Frequency"/>
        <data format="tabular" name="number_output" label="Number of Hbonds Per Time Step"/>
        <data format="tabular" name="time_output" label="Time Steps for Each Observed Hbond"/>
    </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.

_____


.. class:: infomark

**Input**

       - Trajectory file  (DCD).
       - PDB file.
       - Segids of the two segments.
       - cutoff distance and angle.
     
_____

        
.. class:: infomark

**Output**

       - .csv files of the Hbond frequency, number of Hbonds Per time step, and time steps for each observed Hbond


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