<tool id="bio3d_rmsf" name="RMSF Analysis" version="@VERSION@">
    <description>rmsf using Bio3D</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
<![CDATA[ 
    Rscript '$__tool_directory__/rmsf.R' 
        '$dcdin'  
        '$pdbin'
        #if $rmsf.sele == 'calpha':
          "string"
          "calpha"
        #end if
        #if $rmsf.sele == 'cbeta':
          "string"
          '$rmsf.cbeta'
        #end if
        #if $rmsf.sele == 'backbone':
          "string"
          "backbone"
        #end if
        #if $rmsf.sele == 'sidechain':
          "string"
          '$rmsf.sidechain'
        #end if
        #if $rmsf.sele == 'protein':
          "string"
          "protein"
        #end if
        #if $rmsf.sele == 'ligand':
          "string"
          "ligand"
        #end if
        #if $rmsf.sele == 'nucleic':
          "string"
          "nucleic"
        #end if
        #if $rmsf.sele == 'water':
          "string"
          "water"
        #end if
        #if $rmsf.sele == 'hyd':
          "string"
          "hyd"
        #end if
        #if $rmsf.sele == 'noh':
          "string"
          "noh"
        #end if
        #if $rmsf.sele == 'loop':
          "resno"
          '$rmsf.res1'
          '$rmsf.res2'
        #end if
        #if $rmsf.sele == "elety":
          "elety"
          '$rmsf.elety'
        #end if
        #if $rmsf.sele == "resid":
          "resid"
          '$rmsf.resid'
        #end if
        #if $rmsf.sele == "segid":
          "segid"
          '$rmsf.segid'
        #end if
        '$output'
        '$rmsf_plot' 
    2>&1
]]></command>
    <inputs>
       <expand macro="analysis_inputs"/>
        <conditional name="rmsf">
           <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="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">Resid</option>
             <option value="segid">Segid</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="Resid of the loop starting residue"/>
             <param name="res2" type="text" label="Resid of the loop ending residue"/>
           </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="Resid"/>
          </when>
          <when value="segid">
            <param name="segid"  type="text" value="SUBS" label="Segid"/>
          </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="rmsf raw data"/>
        <data format="png" name="rmsf_plot" label="rmsf plot"/>
    </outputs>
    <tests>
        <test>
            <expand macro="tests_inputs"/>
            <param name="sele" value="calpha"/>
            <output name="output" file="rmsf_raw_data.tabular" /> 
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

The Root Mean Square Fluctuation (RMSF) conformational variance that analysis can analyze the
portions of structure that are fluctuating from their mean structure the most (or least). This tool can calculate and plot the RMSF of the selected section.

_____

.. class:: infomark

**Input**

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

_____

.. class:: infomark

**Output**

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


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