annotate dihedrals.xml @ 8:f55dd7c08112 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"

<tool id="mdanalysis_dihedral" name="Dihedral Analysis" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
    <description>Time series of dihedrals</description>
    <macros>
        <import>macros.xml</import>
        <token name="@GALAXY_VERSION@">0</token>
    </macros>   
    <expand macro="requirements" />
    <command detect_errors="exit_code">
<![CDATA[
    python '$__tool_directory__/dihedrals.py'
        --itraj '$trajin' 
        --istr '$strin' 
        --itrajext '$trajin.ext'
        --istrext '$strin.ext'
        --isegid1 '$segid1' 
        --iresid1 '$resid1' 
        --iname1 '$name1' 
        --isegid2 '$segid2' 
        --iresid2 '$resid2'
        --iname2 '$name2' 
        --isegid3 '$segid3' 
        --iresid3 '$resid3'
        --iname3 '$name3' 
        --isegid4 '$segid4' 
        --iresid4 '$resid4' 
        --iname4 '$name4'
        --output '$output'  
        --odihedral_plot '$dihedral_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="segid3"  type="text" value="HET" label="Segment ID of atom 3"/>
        <param name="resid3"  type="text" value="3" label="Residue ID of atom 3"/>
        <param name="name3"  type="text" value="C2" label="Atom name of atom 3"/>
        <param name="segid4"  type="text" value="HET" label="Segment ID of atom 4"/>
        <param name="resid4"  type="text" value="3" label="Residue ID of atom 4"/>
        <param name="name4"  type="text" value="C3" label="Atom name of atom 4"/>
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="Dihedral analysis raw data"/>
        <data format="png" name="dihedral_plot" label="Dihedral 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="segid3" value="HET"/>
            <param name="resid3" value="3"/>
            <param name="name3" value="C2"/>
            <param name="segid4" value="HET"/>
            <param name="resid4" value="3"/>
            <param name="name4" value="C3"/>
            <output name="output" file="Dihedral_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"/>
            <param name="segid3" value="SYSTEM"/>
            <param name="resid3" value="3"/>
            <param name="name3" value="C2"/>
            <param name="segid4" value="SYSTEM"/>
            <param name="resid4" value="3"/>
            <param name="name4" value="C3"/>
            <output name="output">
                <assert_contents>
                    <has_n_columns n="2" />
                    <has_line_matching expression="0\t-61.*" />
                    <has_line_matching expression="12\t-76.*" />
                    <has_line_matching expression="4\t-66.*" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**
        
This tool calculates and plots dihedral angles (angle between two intersecting planes) between four atoms.

_____


.. class:: infomark

**Input**

       - Trajectory file  (DCD).
       - PDB file.
       - Segment IDs, residue IDs and names of the four atoms to calculate the dihedral angle.

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 the dihedral angle calculated for each frame.
       - Image (as png) of the time series graph.

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