<tool id="mdanalysis_cosine_analysis" name="Cosine Content" version="@VERSION@">
    <description>Measure the cosine content of the PCA projection</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
<![CDATA[
     python '$__tool_directory__/pca_cosine.py' 
        --idcd '$dcdin' 
        --ipdb '$pdbin'
        --icomponents '$components'
        --iindex '$index' 
        --output '$output' 
        --cosout '$cosout'
    2>&1
]]></command>
    <inputs>
        <expand macro="analysis_inputs"/>
        <param name="components"  type="integer" value="3" label="Number of components"/>
        <param name="index"  type="integer" value="0" label="The index of the PCA component projection to be analyzed"/>
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="PCA Analysis raw data"/>
        <data format="txt" name="cosout" label="Cosine content of the PCA projection"/>
    </outputs>
    <tests>
        <test>
            <expand macro="tests_inputs"/>
            <param name="components" value="3"/>
            <param name="index" value="0"/>
            <output name="cosout">
              <assert_contents>
                <has_text text="0.5832533" />
              </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**
        
The cosine content of the principal components is a good indicator for determine good or bad sampling and can be use to determine the convergence of the MD simulation.
This tool can calculate the cosine content of a user define PCA projection.
This tool use zero based indexes (0 is PC1).  
    
_____


.. class:: infomark

**Input**

       - Trajectory file  (DCD).
       - PDB file.

_____

        
.. class:: infomark

**Output**

       - The cosine content value.
       - Tab-separated file of raw data of first three principle component.

    ]]></help>
      <expand macro="citations">
          <citation type="doi">10.1103/PhysRevE.65.031910</citation>
      </expand>
</tool>