<tool id="bio3d_rmsf" name="RMSF Analysis" version="@VERSION@">
    <description> using Bio3D</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
<![CDATA[ 
    Rscript '$__tool_directory__/rmsf.R' 
        '$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">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="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" >
              <assert_contents>
                <has_line_matching expression="1\t0.297.*" />
                <has_line_matching expression="418\t0.410.*" />
                <has_line_matching expression="433\t0.300.*" />
              </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

The Root Mean Square Fluctuation (RMSF) provides a measure of conformational variance i.e. which
portions of structure are fluctuating from their mean structure the most (or least). 
This tool can calculate and plot the RMSF 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 RMSF plot
       - Tab-separated file of raw data


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