Mercurial > repos > chemteam > mdanalysis_hbonds

annotate hbonds.xml @ 3:fb99a68cf6a3 draft default tip

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
author chemteam
date Wed, 20 May 2020 16:55:40 +0000
parents 525e4dd613fc
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1 <tool id="mdanalysis_hbonds" name="Hydrogen Bond Analysis" version="@VERSION@">
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525e4dd613fc "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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2 <description>- analyze H-bonds between two segments</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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525e4dd613fc "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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7 <requirement type="package" version="0.25.1">pandas</requirement>
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8 </expand>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 python '$__tool_directory__/hbonds.py'
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525e4dd613fc "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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12 --itraj '$trajin'
525e4dd613fc "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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13 --istr '$strin'
525e4dd613fc "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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14 --itrajext '$trajin.ext'
525e4dd613fc "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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15 --istrext '$strin.ext'
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16 --isegid1 '$segid1'
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17 --isegid2 '$segid2'
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18 --idistance '$distance'
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19 --iangle '$angle'
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20 --output '$output'
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21 --ofreq_output '$freq_output'
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22 --onumber_output '$number_output'
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23 --otime_output '$time_output'
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24 2>&1
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25 ]]></command>
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26 <inputs>
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27 <expand macro="analysis_inputs"/>
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28 <param name="segid1" type="text" value="PRO" label="Segment ID of selection 1"/>
525e4dd613fc "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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29 <param name="segid2" type="text" value="HET" label="Segment ID of selection 2"/>
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30 <param name="distance" type="float" value="3.0" label="Cutoff distance"/>
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31 <param name="angle" type="float" value="120.0" label="Cutoff angle"/>
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32 </inputs>
bad21f113679 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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33 <outputs>
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34 <data format="tabular" name="output" label="H-bond analysis raw data"/>
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35 <data format="tabular" name="freq_output" label="H-bond frequency"/>
525e4dd613fc "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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36 <data format="tabular" name="number_output" label="Number of H-bonds per time step"/>
525e4dd613fc "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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37 <data format="tabular" name="time_output" label="Time steps for each observed H-bond"/>
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38 </outputs>
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39 <tests>
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40 <test>
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41 <expand macro="tests_inputs"/>
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42 <param name="distance" value="3.0"/>
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43 <param name="angle" value="120.0"/>
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44 <output name="number_output">
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45 <assert_contents>
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46 <has_text text="1.000" />
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47 </assert_contents>
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48 </output>
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49 </test>
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50 </tests>
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51 <help><![CDATA[
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52 .. class:: infomark
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53
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54 **What it does**
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55
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56 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.
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57
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58 _____
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59
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60
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61 .. class:: infomark
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62
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63 **Input**
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64
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65 - Trajectory file (DCD).
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66 - PDB file.
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67 - Segment IDs of the two segments.
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68 - Cutoff distance and angle.
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69
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70 _____
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71
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72
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73 .. class:: infomark
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74
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75 **Output**
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76
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77 - Tabular files containing H-bond frequency, number of H-bonds Per time step, and time steps for each observed H-bond.
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78
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79
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80 ]]></help>
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81 <expand macro="citations" />
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82 </tool>