annotate ramachandran_plots.xml @ 2:b348dfa55e0a draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"

<tool id="mdanalysis_ramachandran_plot" name="Ramachandran Plots" version="@VERSION@">
    <description>- calculate and plot the distribution of two dihedrals in a trajectory</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.3.1">scipy</requirement>
        <requirement type="package" version="0.9.0">seaborn</requirement>
        <requirement type="package" version="1.1.0">nbdime</requirement>
    </expand>
    <command detect_errors="exit_code">
<![CDATA[
    python '$__tool_directory__/ramachandran_plots.py'
        --itraj '$trajin' 
        --istr '$strin'
        --itrajext '$trajin.ext'
        --istrext '$strin.ext'
        --isegid1  '$phi.phi_segid1'
        --iresid1  '$phi.phi_resid1' 
        --iname1   '$phi.phi_name1'
        --isegid2  '$phi.phi_segid2'
        --iresid2  '$phi.phi_resid2' 
        --iname2   '$phi.phi_name2'
        --isegid3  '$phi.phi_segid3'
        --iresid3  '$phi.phi_resid3' 
        --iname3   '$phi.phi_name3'
        --isegid4  '$phi.phi_segid4'
        --iresid4  '$phi.phi_resid4' 
        --iname4   '$phi.phi_name4'
        --isegid5  '$psi.psi_segid1'
        --iresid5  '$psi.psi_resid1' 
        --iname5   '$psi.psi_name1'
        --isegid6  '$psi.psi_segid2'
        --iresid6  '$psi.psi_resid2' 
        --iname6   '$psi.psi_name2' 
        --isegid7  '$psi.psi_segid3' 
        --iresid7  '$psi.psi_resid3' 
        --iname7   '$psi.psi_name3' 
        --isegid8  '$psi.psi_segid4' 
        --iresid8  '$psi.psi_resid4' 
        --iname8   '$psi.psi_name4' 
        --output   '$output'  
        --oramachandran_plot '$ramachandran_plot'
    2>&1
]]></command>
    <inputs>
        <expand macro="analysis_inputs"/>
        <section name="phi" title="Phi" expanded="False">
          <param name="phi_segid1"  type="text" value="HET" label="Segment ID of atom 1">
            <expand macro="sanitizer"/>
          </param>
          <param name="phi_resid1"  type="text" value="3" label="Residue ID of atom 1">
            <expand macro="sanitizer_resids"/>
          </param>
          <param name="phi_name1"  type="text" value="O5" label="Atom name of atom 1">
            <expand macro="sanitizer"/>
          </param>
          <param name="phi_segid2"  type="text" value="HET" label="Segment ID of atom 2">
            <expand macro="sanitizer"/>
          </param>
          <param name="phi_resid2"  type="text" value="3" label="Residue ID of atom 2">
            <expand macro="sanitizer_resids"/>
          </param>
          <param name="phi_name2"  type="text" value="C1" label="Atom name of atom 2">
            <expand macro="sanitizer"/>
          </param>
          <param name="phi_segid3"  type="text" value="HET" label="Segment ID of atom 3">
            <expand macro="sanitizer"/>
          </param>
          <param name="phi_resid3"  type="text" value="2" label="Residue ID of atom 3">
            <expand macro="sanitizer_resids"/>
          </param>
          <param name="phi_name3"  type="text" value="O4" label="Atom name of atom 3">
            <expand macro="sanitizer"/>
          </param>
          <param name="phi_segid4"  type="text" value="HET" label="Segment ID of atom 4">
            <expand macro="sanitizer"/>
          </param>
          <param name="phi_resid4"  type="text" value="2" label="Residue ID of atom 4">
            <expand macro="sanitizer_resids"/>
          </param>
          <param name="phi_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="psi_segid1"  type="text" value="HET" label="Segment ID of atom 1">
            <expand macro="sanitizer"/>
          </param>
          <param name="psi_resid1"  type="text" value="3" label="Residue ID of atom 1">
            <expand macro="sanitizer_resids"/>
          </param>
          <param name="psi_name1"  type="text" value="C1" label="Atom name of atom 1">
            <expand macro="sanitizer"/>
          </param>
          <param name="psi_segid2"  type="text" value="HET" label="Segment ID of atom 2">
            <expand macro="sanitizer"/>
          </param>
          <param name="psi_resid2"  type="text" value="2" label="Residue ID of atom 2">
            <expand macro="sanitizer_resids"/>
          </param>
          <param name="psi_name2"  type="text" value="O4" label="Atom name of atom 2">
            <expand macro="sanitizer"/>
          </param>
          <param name="psi_segid3"  type="text" value="HET" label="Segment ID of atom 3">
            <expand macro="sanitizer"/>
          </param>
          <param name="psi_resid3"  type="text" value="2" label="Residue ID of atom 3">
            <expand macro="sanitizer_resids"/>
          </param>
          <param name="psi_name3"  type="text" value="C4" label="Atom name of atom 3">
            <expand macro="sanitizer"/>
          </param>
          <param name="psi_segid4"  type="text" value="HET" label="Segment ID of atom 4">
            <expand macro="sanitizer"/>
          </param>
          <param name="psi_resid4"  type="text" value="2" label="Residue ID of atom 4">
            <expand macro="sanitizer_resids"/>
          </param>
          <param name="psi_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>
        <test>
            <expand macro="tests_inputs_gmx"/>
            <param name="phi_segid1" value="SYSTEM"/>
            <param name="phi_resid1" value="3"/>
            <param name="phi_name1" value="O5"/>
            <param name="phi_segid2" value="SYSTEM"/>
            <param name="phi_resid2" value="3"/>
            <param name="phi_name2" value="C1"/>
            <param name="phi_segid3" value="SYSTEM"/>
            <param name="phi_resid3" value="2"/>
            <param name="phi_name3" value="O4"/>
            <param name="phi_segid4" value="SYSTEM"/>
            <param name="phi_resid4" value="2"/>
            <param name="phi_name4" value="C4"/>
            <param name="psi_segid1" value="SYSTEM"/>
            <param name="psi_resid1" value="3"/>
            <param name="psi_name1" value="C1"/>
            <param name="psi_segid2" value="SYSTEM"/>
            <param name="psi_resid2" value="2"/>
            <param name="psi_name2" value="O4"/>
            <param name="psi_segid3" value="SYSTEM"/>
            <param name="psi_resid3" value="2"/>
            <param name="psi_name3" value="C4"/>
            <param name="psi_segid4" value="SYSTEM"/>
            <param name="psi_resid4" value="2"/>
            <param name="psi_name4" value="C3"/>
            <output name="output" file="Ramachandran_Plot_raw_data_gmx.tabular" />
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**
        
A Ramachandran plot ([φ,ψ] plot) was originally developed as a way to visualize the energetically allowed regions for backbone dihedral angles ψ and φ of an amino acid.
It 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-defined φ and ψ angles of a trajectory. 

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

_____


.. class:: infomark

**Input**

       - Trajectory file  (DCD).
       - PDB file.
       - Segment IDs, residue IDs and names of the four atoms to calculate dihedrals.

Note that a MDAnalysis 'segment' is a larger organizational unit, for example one protein or all the solvent molecules or simply the whole system.

_____

        
.. class:: infomark

**Output**

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


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