Mercurial > repos > chemteam > mdanalysis_hbonds
view hbonds.xml @ 2:d23ef0663267 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
author | chemteam |
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date | Thu, 06 Feb 2020 19:41:49 -0500 |
parents | 5c38e38dbc35 |
children | 4c36f5ad2799 |
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<tool id="mdanalysis_hbonds" name="Hydrogen Bond Analysis" version="@VERSION@"> <description>- analyze H-bonds between two segments</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> <requirement type="package" version="0.25.1">pandas</requirement> </expand> <command detect_errors="exit_code"> <![CDATA[ python '$__tool_directory__/hbonds.py' --itraj '$trajin' --istr '$strin' --itrajext '$trajin.ext' --istrext '$strin.ext' --isegid1 '$segid1' --isegid2 '$segid2' --idistance '$distance' --iangle '$angle' --output '$output' --ofreq_output '$freq_output' --onumber_output '$number_output' --otime_output '$time_output' 2>&1 ]]></command> <inputs> <expand macro="analysis_inputs"/> <param name="segid1" type="text" value="PRO" label="Segment ID of selection 1"/> <param name="segid2" type="text" value="HET" label="Segment ID of selection 2"/> <param name="distance" type="float" value="3.0" label="Cutoff distance"/> <param name="angle" type="float" value="120.0" label="Cutoff angle"/> </inputs> <outputs> <data format="tabular" name="output" label="H-bond analysis raw data"/> <data format="tabular" name="freq_output" label="H-bond frequency"/> <data format="tabular" name="number_output" label="Number of H-bonds per time step"/> <data format="tabular" name="time_output" label="Time steps for each observed H-bond"/> </outputs> <tests> <test> <expand macro="tests_inputs"/> <param name="distance" value="3.0"/> <param name="angle" value="120.0"/> <output name="number_output"> <assert_contents> <has_text text="1.000" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** This tool calculates hydrogen bonds between two segments of the system. 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 **Input** - Trajectory file (DCD). - PDB file. - Segment IDs of the two segments. - Cutoff distance and angle. _____ .. class:: infomark **Output** - Tabular files containing H-bond frequency, number of H-bonds Per time step, and time steps for each observed H-bond. ]]></help> <expand macro="citations" /> </tool>