Mercurial > repos > chemteam > mdanalysis_ramachandran_plot
view ramachandran_plots.xml @ 3:8bd0e29927da draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
author | chemteam |
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date | Wed, 20 May 2020 13:03:30 -0400 |
parents | ce0728b92289 |
children | 70a2d548e62c |
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<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>