Mercurial > repos > chemteam > mdanalysis_ramachandran_plot
diff ramachandran_plots.xml @ 1:ce0728b92289 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
| author | chemteam |
|---|---|
| date | Mon, 07 Oct 2019 12:50:22 -0400 |
| parents | d710c7f00ae6 |
| children | 70a2d548e62c |
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--- a/ramachandran_plots.xml Wed Apr 03 15:46:32 2019 -0400 +++ b/ramachandran_plots.xml Mon Oct 07 12:50:22 2019 -0400 @@ -1,42 +1,44 @@ -<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> +<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="1.2.1">scipy</requirement> + <requirement type="package" version="1.3.1">scipy</requirement> <requirement type="package" version="0.9.0">seaborn</requirement> - <requirement type="package" version="1.0.5">nbdime</requirement> + <requirement type="package" version="1.1.0">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 '$psi.name4' + --itraj '$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 @@ -44,78 +46,78 @@ <inputs> <expand macro="analysis_inputs"/> <section name="phi" title="Phi" expanded="False"> - <param name="segid1" type="text" value="HET" label="Segid of atom 1"> + <param name="phi_segid1" type="text" value="HET" label="Segment ID of atom 1"> <expand macro="sanitizer"/> </param> - <param name="resid1" type="text" value="3" label="Resid of atom 1"> + <param name="phi_resid1" type="text" value="3" label="Residue ID of atom 1"> <expand macro="sanitizer_resids"/> </param> - <param name="name1" type="text" value="O5" label="Atom name of atom 1"> + <param name="phi_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"> + <param name="phi_segid2" type="text" value="HET" label="Segment ID of atom 2"> <expand macro="sanitizer"/> </param> - <param name="resid2" type="text" value="3" label="Resid of atom 2"> + <param name="phi_resid2" type="text" value="3" label="Residue ID of atom 2"> <expand macro="sanitizer_resids"/> </param> - <param name="name2" type="text" value="C1" label="Atom name of atom 2"> + <param name="phi_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"> + <param name="phi_segid3" type="text" value="HET" label="Segment ID of atom 3"> <expand macro="sanitizer"/> </param> - <param name="resid3" type="text" value="2" label="Resid of atom 3"> + <param name="phi_resid3" type="text" value="2" label="Residue ID of atom 3"> <expand macro="sanitizer_resids"/> </param> - <param name="name3" type="text" value="O4" label="Atom name of atom 3"> + <param name="phi_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"> + <param name="phi_segid4" type="text" value="HET" label="Segment ID of atom 4"> <expand macro="sanitizer"/> </param> - <param name="resid4" type="text" value="2" label="Resid of atom 4"> + <param name="phi_resid4" type="text" value="2" label="Residue ID of atom 4"> <expand macro="sanitizer_resids"/> </param> - <param name="name4" type="text" value="C4" label="Atom name of atom 4"> + <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="segid1" type="text" value="HET" label="Segid of atom 1"> + <param name="psi_segid1" type="text" value="HET" label="Segment ID of atom 1"> <expand macro="sanitizer"/> </param> - <param name="resid1" type="text" value="3" label="Resid of atom 1"> + <param name="psi_resid1" type="text" value="3" label="Residue ID of atom 1"> <expand macro="sanitizer_resids"/> </param> - <param name="name1" type="text" value="C1" label="Atom name of atom 1"> + <param name="psi_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"> + <param name="psi_segid2" type="text" value="HET" label="Segment ID of atom 2"> <expand macro="sanitizer"/> </param> - <param name="resid2" type="text" value="2" label="Resid of atom 2"> + <param name="psi_resid2" type="text" value="2" label="Residue ID of atom 2"> <expand macro="sanitizer_resids"/> </param> - <param name="name2" type="text" value="O4" label="Atom name of atom 2"> + <param name="psi_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"> + <param name="psi_segid3" type="text" value="HET" label="Segment ID of atom 3"> <expand macro="sanitizer"/> </param> - <param name="resid3" type="text" value="2" label="Resid of atom 3"> + <param name="psi_resid3" type="text" value="2" label="Residue ID of atom 3"> <expand macro="sanitizer_resids"/> </param> - <param name="name3" type="text" value="C4" label="Atom name of atom 3"> + <param name="psi_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"> + <param name="psi_segid4" type="text" value="HET" label="Segment ID of atom 4"> <expand macro="sanitizer"/> </param> - <param name="resid4" type="text" value="2" label="Resid of atom 4"> + <param name="psi_resid4" type="text" value="2" label="Residue ID of atom 4"> <expand macro="sanitizer_resids"/> </param> - <param name="name4" type="text" value="C3" label="Atom name of atom 4"> + <param name="psi_name4" type="text" value="C3" label="Atom name of atom 4"> <expand macro="sanitizer"/> </param> </section> @@ -127,44 +129,71 @@ <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"/> + <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), 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. +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 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/ + - 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/ _____ @@ -175,8 +204,10 @@ - Trajectory file (DCD). - PDB file. - - Segids, resids and names of the four atoms to calculate diheadrals. - + - 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. + _____ @@ -184,8 +215,8 @@ **Output** - - Tab-separated file of raw data of the φ,ψ angles time series. - - Image (as png) of the Ramachandran Plot. + - Tab-separated file of raw data of the φ,ψ angles over time. + - Image (as png) of the Ramachandran plot. ]]></help>