Mercurial > repos > chemteam > mdanalysis_ramachandran_plot
diff ramachandran_plots.xml @ 4:70a2d548e62c draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
| author | chemteam |
|---|---|
| date | Mon, 24 Aug 2020 16:23:14 -0400 |
| parents | ce0728b92289 |
| children |
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--- a/ramachandran_plots.xml Wed May 20 13:03:30 2020 -0400 +++ b/ramachandran_plots.xml Mon Aug 24 16:23:14 2020 -0400 @@ -1,199 +1,64 @@ -<tool id="mdanalysis_ramachandran_plot" name="Ramachandran Plots" version="@VERSION@"> +<tool id="mdanalysis_ramachandran_plot" name="Ramachandran Plots" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> <description>- calculate and plot the distribution of two dihedrals in a trajectory</description> <macros> <import>macros.xml</import> + <token name="@GALAXY_VERSION@">0</token> </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> + <requirement type="package" version="1.5.2">scipy</requirement> + <requirement type="package" version="0.10.0">seaborn</requirement> + <requirement type="package" version="2.0.0">nbdime</requirement> + <requirement type="package" version="5.3.1">pyyaml</requirement> </expand> - <command detect_errors="exit_code"> -<![CDATA[ + <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/ramachandran_plots.py' - --itraj '$trajin' + --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 '$output' + --iyml '$ymlin' + --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> + <expand macro="analysis_inputs" /> + <section name="ymlparam" title="Torsion Parameters" expanded="False"> + <param format="txt" name="ymlin" type="data" label="Torsion parameters in yml format" help="Information in YAML format about the segid, resid, and name for atoms 1-4 of the phi and psi angles. Example formatting included in the main help text"/> </section> </inputs> <outputs> - <data format="tabular" name="output" label="Ramachandran Plot raw data"/> - <data format="png" name="ramachandran_plot" label="Ramachandran Plot"/> + <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" /> + <param name="trajin" value="test.dcd" ftype="dcd" /> + <param name="strin" value="test.pdb" ftype="pdb" /> + <section name="ymlparam"> + <param name="ymlin" value="test.yml" /> + </section> + <output name="output"> + <assert_contents> + <has_text text="-144.503" /> + <has_text text="-140.553" /> + </assert_contents> + </output> + <output name="ramachandran_plot"> + <assert_contents> + <has_size value="18522" delta="2000" /> + </assert_contents> + </output> </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. +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/ _____ @@ -204,13 +69,59 @@ - Trajectory file (DCD). - PDB file. - - Segment IDs, residue IDs and names of the four atoms to calculate dihedrals. + - Text file in YAML format with 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. + - For protein φ and ψ dihedral definitions see https://proteinstructures.com/Structure/Structure/Ramachandran-plot.html + - For glycan φ and ψ dihedral definitions, see + - `Glycan Structure Website`_ - The glycosidic torsion angle definition is adopted from the crystallographic definition; O5-C1-O1-C'x (Φ; phi), C1-O1-C'x-C'x-1 (Ψ; psi), and O1-C'6-C'5-O'5 (ω; omega). The torsion angle between the first residue of the N-glycan chain and the side chain of the asparagine residue is defined as O5-C1-N'D2-C'G (Φ; phi) and C1-N'D2-C'G-C'B (Ψ; psi). The torsion angle between the first residue of the O-glycan chain and the side chain of the serine residue is defined as O5-C1-O'G-C'B (Φ; phi) and C1-O'G-C'B-C'A (Ψ; psi). For threonine residue, OG1 is used instead of OG. The atom names are based on the CHARMM topology. + - `Glycosciences Website`_ - NMR definition - Φ phi: H1-C1-O1-C′X Ψ psi: C1-O1-C′X-H′X ω omega: O1-C′6-C′5-H′5 Crystallographic definition - Φ phi: O5-C1-O1-C′X Ψ psi: C1-O1-C′X-C′X+1 ω omega: O1-C′6-C′5-O′5 + + - An example of a yaml formatted selection for φ-ψ of a small glycoprotein called PROF with a carbohydrate portion called CARA where φ=O5-C1-OG1-CB1 and ψ=C1-OG1-CB-CA for the selected segment and residue ids. + + .. code-block:: yaml + + ramachandran1: + phi: + atom1: + segid: CARA + resid: 1 + name: O5 + atom2: + segid: CARA + resid: 1 + name: C1 + atom3: + segid: PROF + resid: 4 + name: OG1 + atom4: + segid: PROF + resid: 4 + name: CB + psi: + atom1: + segid: CARA + resid: 1 + name: C1 + atom2: + segid: PROF + resid: 4 + name: OG1 + atom3: + segid: PROF + resid: 4 + name: CB + atom4: + segid: PROF + resid: 4 + name: CA + comment: pick visually using VMD using labels. Go to labels, dihedral to see the information about resname resid and atomname and then lookup the segname for ach atom. + _____ - + .. class:: infomark **Output** @@ -218,7 +129,8 @@ - Tab-separated file of raw data of the φ,ψ angles over time. - Image (as png) of the Ramachandran plot. - + .. _`Glycan Structure Website`: http://www.glycanstructure.org/fragment-db/howto + .. _`Glycosciences Website`: http://www.glycosciences.de/tools/glytorsion/ ]]></help> <expand macro="citations" /> </tool>