annotate ramachandran_plots.xml @ 0:d710c7f00ae6 draft

planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1

<tool id="mdanalysis_ramachandran_plot" name="Ramachandran Plots" version="0.1.3">
    <description>Calculate and plot the distribution of two diheadrals in a trajectory</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.2.1">scipy</requirement>
        <requirement type="package" version="0.9.0">seaborn</requirement>
        <requirement type="package" version="1.0.5">nbdime</requirement>
    </expand>
    <command detect_errors="exit_code">
<![CDATA[
    python '$__tool_directory__/ramachandran_plots.py'
        --idcd '$dcdin' 
        --ipdb '$pdbin'
        --isegid1  '$phi.segid1'
        --iresid1  '$phi.resid1' 
        --iname1   '$phi.name1'
        --isegid2  '$phi.segid2'
        --iresid2  '$phi.resid2' 
        --iname2   '$phi.name2'
        --isegid3  '$phi.segid3'
        --iresid3  '$phi.resid3' 
        --iname3   '$phi.name3'
        --isegid4  '$phi.segid4'
        --iresid4  '$phi.resid4' 
        --iname4   '$phi.name4'
        --isegid5  '$psi.segid1'
        --iresid5  '$psi.resid1' 
        --iname5   '$psi.name1'
        --isegid6  '$psi.segid2'
        --iresid6  '$psi.resid2' 
        --iname6   '$psi.name2' 
        --isegid7  '$psi.segid3' 
        --iresid7  '$psi.resid3' 
        --iname7   '$psi.name3' 
        --isegid8  '$psi.segid4' 
        --iresid8  '$psi.resid4' 
        --iname8   '$psi.name4' 
        --output   '$output'  
        --oramachandran_plot '$ramachandran_plot'
    2>&1
]]></command>
    <inputs>
        <expand macro="analysis_inputs"/>
        <section name="phi" title="Phi" expanded="False">
          <param name="segid1"  type="text" value="HET" label="Segid of atom 1">
            <expand macro="sanitizer"/>
          </param>
          <param name="resid1"  type="text" value="3" label="Resid of atom 1">
            <expand macro="sanitizer_resids"/>
          </param>
          <param name="name1"  type="text" value="O5" label="Atom name of atom 1">
            <expand macro="sanitizer"/>
          </param>
          <param name="segid2"  type="text" value="HET" label="Segid of atom 2">
            <expand macro="sanitizer"/>
          </param>
          <param name="resid2"  type="text" value="3" label="Resid of atom 2">
            <expand macro="sanitizer_resids"/>
          </param>
          <param name="name2"  type="text" value="C1" label="Atom name of atom 2">
            <expand macro="sanitizer"/>
          </param>
          <param name="segid3"  type="text" value="HET" label="Segid of atom 3">
            <expand macro="sanitizer"/>
          </param>
          <param name="resid3"  type="text" value="2" label="Resid of atom 3">
            <expand macro="sanitizer_resids"/>
          </param>
          <param name="name3"  type="text" value="O4" label="Atom name of atom 3">
            <expand macro="sanitizer"/>
          </param>
          <param name="segid4"  type="text" value="HET" label="Segid of atom 4">
            <expand macro="sanitizer"/>
          </param>
          <param name="resid4"  type="text" value="2" label="Resid of atom 4">
            <expand macro="sanitizer_resids"/>
          </param>
          <param name="name4"  type="text" value="C4" label="Atom name of atom 4">
            <expand macro="sanitizer"/>
          </param>
        </section>
        <section name="psi" title="Psi" expanded="False">
          <param name="segid1"  type="text" value="HET" label="Segid of atom 1">
            <expand macro="sanitizer"/>
          </param>
          <param name="resid1"  type="text" value="3" label="Resid of atom 1">
            <expand macro="sanitizer_resids"/>
          </param>
          <param name="name1"  type="text" value="C1" label="Atom name of atom 1">
            <expand macro="sanitizer"/>
          </param>
          <param name="segid2"  type="text" value="HET" label="Segid of atom 2">
            <expand macro="sanitizer"/>
          </param>
          <param name="resid2"  type="text" value="2" label="Resid of atom 2">
            <expand macro="sanitizer_resids"/>
          </param>
          <param name="name2"  type="text" value="O4" label="Atom name of atom 2">
            <expand macro="sanitizer"/>
          </param>
          <param name="segid3"  type="text" value="HET" label="Segid of atom 3">
            <expand macro="sanitizer"/>
          </param>
          <param name="resid3"  type="text" value="2" label="Resid of atom 3">
            <expand macro="sanitizer_resids"/>
          </param>
          <param name="name3"  type="text" value="C4" label="Atom name of atom 3">
            <expand macro="sanitizer"/>
          </param>
          <param name="segid4"  type="text" value="HET" label="Segid of atom 4">
            <expand macro="sanitizer"/>
          </param>
          <param name="resid4"  type="text" value="2" label="Resid of atom 4">
            <expand macro="sanitizer_resids"/>
          </param>
          <param name="name4"  type="text" value="C3" label="Atom name of atom 4">
            <expand macro="sanitizer"/>
          </param>
        </section>
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="Ramachandran Plot raw data"/>
        <data format="png" name="ramachandran_plot" label="Ramachandran Plot"/>
    </outputs>
    <tests>
        <test>
            <expand macro="tests_inputs"/>
            <param name="phi.segid1" value="HET"/>
            <param name="phi.resid1" value="3"/>
            <param name="phi.name1" value="O5"/>
            <param name="phi.segid2" value="HET"/>
            <param name="phi.resid2" value="3"/>
            <param name="phi.name2" value="C1"/>
            <param name="phi.segid3" value="HET"/>
            <param name="phi.resid3" value="2"/>
            <param name="phi.name3" value="O4"/>
            <param name="phi.segid4" value="HET"/>
            <param name="phi.resid4" value="2"/>
            <param name="phi.name4" value="C4"/>
            <param name="psi.segid1" value="HET"/>
            <param name="psi.resid1" value="3"/>
            <param name="psi.name1" value="C1"/>
            <param name="psi.segid2" value="HET"/>
            <param name="psi.resid2" value="2"/>
            <param name="psi.name2" value="O4"/>
            <param name="psi.segid3" value="HET"/>
            <param name="psi.resid3" value="2"/>
            <param name="psi.name3" value="C4"/>
            <param name="psi.segid4" value="HET"/>
            <param name="psi.resid4" value="2"/>
            <param name="psi.name4" value="C3"/>
            <output name="output" file="Ramachandran_Plot_raw_data.tabular" />
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**
        
A Ramachandran plot ([φ,ψ] plot), originally developed as a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid.
This can be also used to calculate glycosidic φ and ψ angles formed between carbohydrates. This tool can calculate and plot the histogram (ramachandran plot) of user define φ and ψ angles of a trajectory. 

  - For protien φ and ψ diheadral definitions see https://proteinstructures.com/Structure/Structure/Ramachandran-plot.html.
 
  - For glycan φ and ψ diheadral definitions see http://www.glycanstructure.org/

_____


.. class:: infomark

**Input**

       - Trajectory file  (DCD).
       - PDB file.
       - Segids, resids and names of the four atoms to calculate diheadrals.
     
_____

        
.. class:: infomark

**Output**

       - Tab-separated file of raw data of the φ,ψ angles time series.
       - Image (as png) of the Ramachandran Plot.


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