annotate rdf.xml @ 7:1a220575ad7a draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"

<tool id="mdanalysis_rdf" name="RDF Analysis" version="@VERSION@">
    <description>- Radial Distribution Function between two atoms</description>
    <macros>
        <import>macros.xml</import>
    </macros>   
    <expand macro="requirements" />
    <command detect_errors="exit_code">
<![CDATA[
    python '$__tool_directory__/rdf.py' 
        --itraj '$trajin' 
        --istr '$strin' 
        --itrajext '$trajin.ext'
        --istrext '$strin.ext'
        --isegid1 '$segid1'
        --iresid1 '$resid1'
        --iname1 '$name1' 
        --isegid2 '$segid2'
        --iresid2 '$resid2'
        --iname2 '$name2'
        --inbins '$nbins'
        --istart '$start' 
        --iend '$end' 
        --output '$output' 
        --ordf_plot '$rdf_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"/>
        <param name="nbins"  type="text" value="100" label="Number of bins in the histogram"/>
        <param name="start"  type="text" min="0.0" value="0.0" label="Starting point (angstroms)"
            help="Minimum value of r to calculate RDF for"/>
        <param name="end"  type="text" value="15.0" label="End point (angstroms)"
            help="Maximum value of r to calculate RDF for"/>
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="RDF raw data"/>
        <data format="png" name="rdf_plot" label="RDF 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"/>
            <param name="nbins" value="100"/>
            <param name="start" value="0.0"/>
            <param name="end" value="5.0"/>
            <output name="output">
              <assert_contents>
                <has_n_columns n="2" />
                <not_has_text text="nan" />
                <has_line_matching expression="3.625\s+5171.93.*" />
              </assert_contents>
            </output>
        </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"/>
            <param name="nbins" value="100"/>
            <param name="start" value="0.0"/>
            <param name="end" value="5.0"/>
            <output name="output">
              <assert_contents>
                <has_n_columns n="2" />
                <not_has_text text="nan" />
                <has_line_matching expression="3.275\s+6336.*" />
              </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**
        
The Radial Distribution Function (RDF), g(r), also called pair distribution function or pair correlation function, can be used to find how density varies as a function of distance from a reference atom. 

_____


.. class:: infomark

**Input**

       - Trajectory file (DCD).
       - PDB file.
       - Segment IDs, residue IDs and names of two atoms to calculate RDF values.

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

Other parameters can also be specified: the number of bins in the RDF histogram, and the start and end points for the calculation (i.e. the values of r between which RDF will be calculated).
_____

        
.. class:: infomark

**Output**

       - Tab-separated file of raw data of the RDF.
       - Image (as png) of the RDF plot.

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