<tool id="bio3d_pca_visualize" name="PCA visualization" version="@VERSION@">
    <description>Generate trajectories of principle components of motions</description>
    <macros>
        <import>macros.xml</import>
    </macros>   
    <expand macro="requirements" />
    <command detect_errors="exit_code">
<![CDATA[ 
   Rscript '$__tool_directory__/visualize_pc.R'
        '$dcdin' 
        '$pdbin'
        '$method'
        #if $pca.sele == 'calpha':
          "string"
           "calpha"
        #end if
        #if $pca.sele == 'cbeta':
          "string"
          '$pca.cbeta'
        #end if
        #if $pca.sele == 'backbone':
          "string"
          "backbone"
        #end if
        #if $pca.sele == 'sidechain':
          "string"
          "sidechain"
        #end if
        #if $pca.sele == 'protein':
          "string"
          "protein"
        #end if
        #if $pca.sele == 'ligand':
          "string"
          "ligand"
        #end if
        #if $pca.sele == 'nucleic':
          "string"
          "nucleic"
        #end if
        #if $pca.sele == 'elety':
          "elety"
          '$pca.elety'
        #end if
        #if $pca.sele == 'resid':
          "resid"
          '$pca.resid'
        #end if
        #if $pca.sele == 'segid':
          "segid"
          '$pca.segid'
        #end if
        '$pc_id' 
        '$pdbout' 
    2>&1
]]></command>
    <inputs>
        <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 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>
        <param name="pc_id" type="integer" value="1" label="Principle component id"/>
    </inputs>
    <outputs>
        <data format="pdb" name="pdbout" label="PCA_${pc_id}.pdb"/>
    </outputs>
    <tests>
         <test>
            <expand macro="tests_inputs"/>
            <param name="method" value="false"/>
            <param name="sele" value="calpha"/> 
            <param name="pc_id" value="1"/>
            <output name="pdbout" file="PCA_1.pdb" />
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**
        
This tool can generate small trajectories of a given principle component.
      
_____


.. class:: infomark

**Input**

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

_____


.. class:: infomark

**Output**

       - A short trajectory (as PDB) of the given priciple component id.


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