comparison dccm.xml @ 2:c9ae0c833ded draft default tip

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

1:18440ff54f63

<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_35">r-lattice</requirement>
    </expand>
    <command detect_errors="exit_code">
<![CDATA[ 
   Rscript '$__tool_directory__/dccm.R'
        '$dcdin' 

]]></command>
    <inputs>
        <expand macro="analysis_inputs"/>
        <conditional name="dccm">
           <param name="sele" type="select" label="Select domains">
             <option value="calpha">Calpha</option>
             <option value="cbeta">Cbeta</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">Resid</option>
             <option value="segid">Segid</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="Resid"/>
            </when>
            <when value="segid">
                <param name="segid"  type="text" value="SUBS" label="Segid"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="DCCM raw data"/>

.. 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. The negative values (negative correlation) indicate the atoms moves in opposite directions and the positive values (positive correlation) indicate the atoms moves in same directions.
      
_____


.. 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>

2:c9ae0c833ded

<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' 

]]></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"/>

.. 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>