Mercurial > repos > chemteam > mdanalysis_hbonds

annotate hbonds.xml @ 0:469ad3ea5a5f draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
author chemteam
date Wed, 03 Apr 2019 15:48:18 -0400
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0
469ad3ea5a5f planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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1 <tool id="mdanalysis_hbonds" name="Hydrogen Bond Analysis" version="@VERSION@">
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2 <description>Analyze hbonds 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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7 <requirement type="package" version="0.24.2">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 '$__tool_directory__/hbonds.py'
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12 --idcd '$dcdin'
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13 --ipdb '$pdbin'
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14 --isegid1 '$segid1'
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15 --isegid2 '$segid2'
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16 --idistance '$distance'
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17 --iangle '$angle'
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18 --output '$output'
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19 --ofreq_output '$freq_output'
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20 --onumber_output '$number_output'
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21 --otime_output '$time_output'
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22 2>&1
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23 ]]></command>
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24 <inputs>
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25 <expand macro="analysis_inputs"/>
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26 <param name="segid1" type="text" value="PRO" label="Segid of selection 1"/>
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27 <param name="segid2" type="text" value="HET" label="Segid of selection 2"/>
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28 <param name="distance" type="float" value="3.0" label="Cutoff distance"/>
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29 <param name="angle" type="float" value="120.0" label="Cutoff angle"/>
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30 </inputs>
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31 <outputs>
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32 <data format="tabular" name="output" label="Hbond Analysis raw data"/>
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33 <data format="tabular" name="freq_output" label="Hbond Frequency"/>
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34 <data format="tabular" name="number_output" label="Number of Hbonds Per Time Step"/>
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35 <data format="tabular" name="time_output" label="Time Steps for Each Observed Hbond"/>
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36 </outputs>
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37 <tests>
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38 <test>
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39 <expand macro="tests_inputs"/>
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40 <param name="distance" value="3.0"/>
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41 <param name="angle" value="120.0"/>
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42 <output name="number_output">
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43 <assert_contents>
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44 <has_text text="1.000" />
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45 </assert_contents>
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46 </output>
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47 </test>
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48 </tests>
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49 <help><![CDATA[
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50 .. class:: infomark
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51
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52 **What it does**
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53
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54 This tool calculates hydrogen bonds between two segments of the system.
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55
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56 _____
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57
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58
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59 .. class:: infomark
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60
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61 **Input**
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62
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63 - Trajectory file (DCD).
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64 - PDB file.
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65 - Segids of the two segments.
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66 - cutoff distance and angle.
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67
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68 _____
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69
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70
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71 .. class:: infomark
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72
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73 **Output**
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74
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75 - .csv files of the Hbond frequency, number of Hbonds Per time step, and time steps for each observed Hbond
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76
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77
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78 ]]></help>
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79 <expand macro="citations" />
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80 </tool>