<tool id="bio3d_rmsd" name="RMSD Analysis" version="@VERSION@">
    <description> using Bio3D</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
<![CDATA[ 
     Rscript '$__tool_directory__/rmsd.R'
        '$dcdin'  
        '$pdbin'
        #if $rmsd.sele == 'calpha':
          "string"
          "calpha"
        #end if
        #if $rmsd.sele == 'cbeta':
          "string"
          "cbeta"
        #end if
        #if $rmsd.sele == 'backbone':
          "string"
          "backbone"
        #end if
        #if $rmsd.sele == 'sidechain':
          "string"
          "sidechain"
        #end if
        #if $rmsd.sele == 'protein':
          "string"
          "protein"
        #end if
        #if $rmsd.sele == 'ligand':
          "string"
          "ligand"
        #end if
        #if $rmsd.sele == 'nucleic':
          "string"
          "nucleic"
        #end if
        #if $rmsd.sele == 'water':
          "string"
          "water"
        #end if
        #if $rmsd.sele == 'hyd':
          "string"
          "hyd"
        #end if
        #if $rmsd.sele == 'noh':
          "string"
          "noh"
        #end if
        #if $rmsd.sele == "loop":
          "resno"
          '$rmsd.res1'
          '$rmsd.res2'
        #end if
        #if $rmsd.sele == "elety":
          "elety"
          '$rmsd.elety'
        #end if
        #if $rmsd.sele == "resid":
          "resid"
          '$rmsd.resid'
        #end if
        #if $rmsd.sele == "segid":
          "segid"
          '$rmsd.segid'
        #end if
        '$output'
        '$rmsd_plot' 
        '$rmsd_hist_plot'
    2>&1
]]></command>
    <inputs>
        <expand macro="analysis_inputs"/>
        <conditional name="rmsd">
           <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="loop">Loop</option>
             <option value="water">Water</option>
             <option value="hyd">Hydrogens</option>
             <option value="noh">Non-hydrogens</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="backbone">
           </when> 
           <when value="sidechain">
           </when>
           <when value="protein">
           </when>
           <when value="ligand">
           </when>
           <when value="nucleic">
           </when>
           <when value="loop">
             <param name="res1"  type="text" label="ID of the residue at the start of the loop"/>
             <param name="res2"  type="text" label="ID of the residue at the end of the loop"/>
           </when>
           <when value="water">
           </when>
           <when value="hyd">
          </when>
          <when value="noh">
          </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="RMSD raw data"/>
        <data format="png" name="rmsd_plot" label="RMSD plot"/>
        <data format="png" name="rmsd_hist_plot" label="RMSD histogram plot"/>
    </outputs>
    <tests>
        <test>
            <expand macro="tests_inputs"/>
            <param name="sele" value="calpha"/>
            <output name="output" file="RMSD_raw_data.tabular" />
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

The Root Mean Square Deviation (RMSD) is a standard measure of structural distance between coordinates.
This tool can calculate and plot the RMSD of the selected section of the protein (or other molecule).

_____


.. class:: infomark

**Input**

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

_____


.. class:: infomark

**Output**

       - Image (as PNG) of the RMSD plot.
       - Image (as PNG) of the RMSD histogram plot.
       - Tab-separated file of raw data.

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