Mercurial > repos > chemteam > traj_selections_and_merge
view traj_select_and_merge.xml @ 1:8740338fdff4 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 73aae096eb9df31f7080b1a201882f1f1b571d9b"
author | chemteam |
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date | Wed, 14 Jul 2021 12:43:41 +0000 |
parents | f4a1e92ca3d2 |
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<tool id="traj_selections_and_merge" name="Trajectory select and merge" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> <description>- select specific molecules and merge multiple trajectories.</description> <macros> <import>macros.xml</import> <token name="@GALAXY_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ ln -s '$strin' str.${strin.ext} && #for $trj in $trajs: ln -s '$trj' `basename '$trj'`.${select.traj_fmt} && #end for python '$mdtraj_script' --istr str.${strin.ext} --itraj *.${select.traj_fmt} --isele '$selection' --o_str output.${strin.ext} --o_trj output.${select.traj_fmt} && mv output.${strin.ext} '$outputstr' && mv output.${select.traj_fmt} '$outputtraj' ]]></command> <configfiles> <configfile name="mdtraj_script"><![CDATA[ import mdtraj as md import sys import argparse def parse_command_line(argv): parser = argparse.ArgumentParser() parser.add_argument('--istr', help='input str') parser.add_argument('--itraj', nargs='+', help='input traj') parser.add_argument('--isele', help='selection') parser.add_argument('--o_str', help='MDA Ramachandran plot') parser.add_argument('--o_trj', help='Seaborn Ramachandran plot') return parser.parse_args() args = parse_command_line(sys.argv) list_of_traj = [] if args.itraj is not None: list_of_traj.extend(args.itraj) try: traj = md.load(list_of_traj, top=args.istr) except Exception as einstance: print(type(einstance)) print(einstance.args) print(einstance) topology = traj.topology try: atoms_to_keep = topology.select(str(args.isele)) except Exception as einstance: print("Error: Check the selection is valid for the dataset chosen") print(type(einstance)) print(einstance.args) print(einstance) traj.restrict_atoms(atoms_to_keep) newstruct = traj.slice(1) newstruct.save(args.o_str) traj.save(args.o_trj) ]]></configfile> </configfiles> <inputs> <param format="pdb,gro" name="strin" type="data" label="PDB/GRO input" /> <conditional name="select"> <param name="traj_fmt" type="select" label="Trajectory format" help="Select the trajectory format to filter by"> <option selected="True" value="dcd">dcd</option> <option value="xtc">xtc</option> <option value="netcdf">netcdf</option> <option value="trr">trr</option> </param> <when value="dcd"> <param name="trajs" multiple="True" type="data" format="dcd" label="trajectory file(s) input" /> </when> <when value="xtc"> <param name="trajs" multiple="True" type="data" format="xtc" label="trajectory file(s) input" /> </when> <when value="netcdf"> <param name="trajs" multiple="True" type="data" format="netcdf" label="trajectory file(s) input" /> </when> <when value="trr"> <param name="trajs" multiple="True" type="data" format="trr" label="trajectory file(s) input" /> </when> </conditional> <param name="selection" type="text" value="not water and not segname POT and not segname CLA" label="selection to keep" help="A valid mdtraj style selection string that selects atoms to keep in structure and trajectory file output"> <validator type="regex" message="Maximum of 60 characters and space allowed.">^[a-zA-Z0-9 ]{1,60}$</validator> </param> </inputs> <outputs> <data name="outputstr" format_source="strin" /> <data name="outputtraj" format_source="trajs" /> </outputs> <tests> <test> <param name="strin" value="test.pdb" ftype="pdb" /> <conditional name="select"> <param name="traj_fmt" value="dcd" /> <param name="trajs" value="test.dcd" /> </conditional> <param name="selection" value="not water and not segname SOD and not segname CLA" /> <output name="outputstr"> <assert_contents> <has_text text="ATOM 1 C1 BGL A 1 " /> <has_text text="ATOM 24 HO6 BGL A 1" /> </assert_contents> </output> <output name="outputtraj"> <assert_contents> <has_size value="4000" delta="100" /> </assert_contents> </output> </test> <test> <param name="strin" value="test.gro" ftype="gro" /> <conditional name="select"> <param name="traj_fmt" value="xtc" /> <param name="trajs" value="test.xtc" /> </conditional> <param name="selection" value="resname BGLC" /> <output name="outputstr"> <assert_contents> <has_text text=" 1BGLC C1 1" /> <has_text text=" 1BGLC HO6 24" /> </assert_contents> </output> <output name="outputtraj"> <assert_contents> <has_size value="1812" delta="100" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** This tool is a filter and multijoin for trajectory files. You can select specific molecules (or atoms) and save out a new structure and trajectory file. If there are multiple trajectories selected, then these will all be combined into a single trajectory output. Use this tool to: - reduce the size of trajectories for later analysis and help with selections where analysis tools may not have selection features that you need. - combine trajectories for analysis, this is imperative for proper molecular dynamics analysis. _____ .. class:: infomark **Input** - Structure file (pdb,gro) - Choose a format of trajectory file (trr,xtc, dcd, netcdf) - Trajectory file(s) (the files displayed are filtered by the trajectory type chosen). - A valid mdtraj selection for the system under consideration. For example: not water and segname CARA and not type H _____ .. class:: infomark **Output** - Structure file (same as input format) - Trajectory file (same as input format) ]]></help> <expand macro="citations" /> </tool>