comparison pca.xml @ 5:1414831b3c86 draft default tip

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

4:74ee243060e6

<tool id="bio3d_pca" name="PCA" version="@VERSION@">
    <description>Principle component analysis using Bio3D</description>    
    <macros>
        <import>macros.xml</import>
    </macros>   
    <expand macro="requirements" />
    <command detect_errors="exit_code">

        <expand macro="analysis_inputs"/>
        <param name="method" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
            label="Use singular value decomposition (SVD) instead of default eigenvalue decomposition ?" help="Default: No" />
        <conditional name="pca">
           <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>
           <when value="cbeta">
           </when>

           <when value="ligand">
           </when>
           <when value="nucleic">
           </when>
          <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="PCA raw data"/>

    <help><![CDATA[
.. class:: infomark

**What it does**

PCA can be used to determine the relationship between statistically meaningful conformations (major global motions)
sampled during the trajectory. 

_____


.. class:: infomark

**Input**

       - Input file in PDB format
       - Input file in dcd format

_____


.. class:: infomark

**Output**

       - Image (as PNG) of the pca plot
       - Image (as PNG) of the pca clusterd plot
       - Image (as PNG) of the PC1 plotted on RMSF
       - Tab-separated file of raw data

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

5:1414831b3c86

<tool id="bio3d_pca" name="PCA" version="@VERSION@">
    <description>- principal component analysis using Bio3D</description>    
    <macros>
        <import>macros.xml</import>
    </macros>   
    <expand macro="requirements" />
    <command detect_errors="exit_code">

        <expand macro="analysis_inputs"/>
        <param name="method" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
            label="Use singular value decomposition (SVD) instead of default eigenvalue decomposition ?" help="Default: No" />
        <conditional name="pca">
           <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>
           <when value="cbeta">
           </when>

           <when value="ligand">
           </when>
           <when value="nucleic">
           </when>
          <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="PCA raw data"/>

    <help><![CDATA[
.. class:: infomark

**What it does**

Principal component analysis (PCA) can be used to determine the relationship between statistically meaningful conformations (major global motions)
sampled during the trajectory. 

_____


.. class:: infomark

**Input**

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

_____


.. class:: infomark

**Output**

       - Image (as PNG) of the PCA plot
       - Image (as PNG) of the PCA clustered plot
       - Image (as PNG) of the first principal component plotted on RMSF
       - Tab-separated file of raw data

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