annotate dccm.xml @ 2:c9ae0c833ded draft default tip

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"

<tool id="bio3d_dccm" name="DCCM analysis" version="@VERSION@">
    <description>- Dynamical Cross-Correlation Maps using Bio3D (DCCM)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="0.20_38">r-lattice</requirement>
    </expand>
    <command detect_errors="exit_code">
<![CDATA[ 
   Rscript '$__tool_directory__/dccm.R'
        '$dcdin' 
        '$pdbin'
        #if $dccm.sele == 'calpha':
          "string"
           "calpha"
        #end if
        #if $dccm.sele == 'cbeta':
          "string"
          '$dccm.cbeta'
        #end if
        #if $dccm.sele == 'backbone':
          "string"
          "backbone"
        #end if
        #if $dccm.sele == 'sidechain':
          "string"
          "sidechain"
        #end if
        #if $dccm.sele == 'protein':
          "string"
          "protein"
        #end if
        #if $dccm.sele == 'ligand':
          "string"
          "ligand"
        #end if
        #if $dccm.sele == 'nucleic':
          "string"
          "nucleic"
        #end if
        #if $dccm.sele == 'elety':
          "elety"
          '$dccm.elety'
        #end if
        #if $dccm.sele == 'resid':
          "resid"
          '$dccm.resid'
        #end if
        #if $dccm.sele == 'segid':
          "segid"
          '$dccm.segid'
        #end if
        '$output'
        '$dccm_plot'
    2>&1
]]></command>
    <inputs>
        <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>
           </param>
           <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>
            <when value="resid">
                <param name="resid"  type="text" value="BGLC" label="Residue ID"/>
            </when>
            <when value="segid">
                <param name="segid"  type="text" value="SUBS" label="Segment ID"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="DCCM raw data"/>
        <data format="png" name="dccm_plot" label="DCCM plot"/>
    </outputs>
    <tests>
        <test>
            <expand macro="tests_inputs"/>
            <param name="sele" value="calpha"/>
            <output name="dccm_plot" file="dccm_plot.png" compare="sim_size" delta="20000" />
        </test>
    </tests>
    <help><![CDATA[
.. 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**

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

_____

        
.. class:: infomark

**Output**

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

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