view dccm.xml @ 2:c9ae0c833ded draft default tip

"planemo upload for repository commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:44:45 -0400
parents 18440ff54f63
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<tool id="bio3d_dccm" name="DCCM analysis" version="@VERSION@">
    <description>- Dynamical Cross-Correlation Maps using Bio3D (DCCM)</description>
    <expand macro="requirements">
        <requirement type="package" version="0.20_38">r-lattice</requirement>
    <command detect_errors="exit_code">
   Rscript '$__tool_directory__/dccm.R'
        #if $dccm.sele == 'calpha':
        #end if
        #if $dccm.sele == 'cbeta':
        #end if
        #if $dccm.sele == 'backbone':
        #end if
        #if $dccm.sele == 'sidechain':
        #end if
        #if $dccm.sele == 'protein':
        #end if
        #if $dccm.sele == 'ligand':
        #end if
        #if $dccm.sele == 'nucleic':
        #end if
        #if $dccm.sele == 'elety':
        #end if
        #if $dccm.sele == 'resid':
        #end if
        #if $dccm.sele == 'segid':
        #end if
        <expand macro="analysis_inputs"/>
        <conditional name="dccm">
           <param name="sele" type="select" label="Select domains">
             <option value="calpha">C-alpha</option>
             <option value="cbeta">C-beta</option>
             <option value="backbone">Backbone</option>
             <option value="sidechain">Sidechain</option>
             <option value="protein">Protein</option>
             <option value="ligand">Ligand</option>
             <option value="nucleic">Nucleic acids</option>
             <option value="elety">Atom names</option>
             <option value="resid">Residue ID</option>
             <option value="segid">Segment ID</option>
           <when value="calpha"/>
           <when value="cbeta"/>
           <when value="backbone"/>
           <when value="sidechain"/>
           <when value="protein"/>
           <when value="ligand"/>
           <when value="nucleic"/>
           <when value="elety">
                <param name="elety"  type="text" value="CA" label="Atom name"/>
            <when value="resid">
                <param name="resid"  type="text" value="BGLC" label="Residue ID"/>
            <when value="segid">
                <param name="segid"  type="text" value="SUBS" label="Segment ID"/>
        <data format="tabular" name="output" label="DCCM raw data"/>
        <data format="png" name="dccm_plot" label="DCCM plot"/>
            <expand macro="tests_inputs"/>
            <param name="sele" value="calpha"/>
            <output name="dccm_plot" file="dccm_plot.png" compare="sim_size" delta="20000" />
.. class:: infomark

**What it does**
The extent to which the atomic fluctuations/displacements of a system are correlated with one another can be assessed by examining the magnitude of all pairwise cross-correlation coefficients.
The DCCM Analysis tool can plot the atom-wise cross-correlations using the Bio3D package. Negative values (negative correlation) indicate the atoms move in opposite directions, while positive values (positive correlation) indicate the atoms move in the same direction.

.. class:: infomark


       - Input file in PDB format
       - Input file in DCD format


.. class:: infomark


       - Image (as PNG) of the DCCM plot
       - Tab-separated file of raw data

    <expand macro="citations" />