Mercurial > repos > chemteam > mdanalysis_hbonds
comparison hbonds.xml @ 1:5c38e38dbc35 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author | chemteam |
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date | Mon, 07 Oct 2019 12:51:36 -0400 |
parents | 469ad3ea5a5f |
children | 4c36f5ad2799 |
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0:469ad3ea5a5f | 1:5c38e38dbc35 |
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1 <tool id="mdanalysis_hbonds" name="Hydrogen Bond Analysis" version="@VERSION@"> | 1 <tool id="mdanalysis_hbonds" name="Hydrogen Bond Analysis" version="@VERSION@"> |
2 <description>Analyze hbonds between two segments</description> | 2 <description>- analyze H-bonds between two segments</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"> | 6 <expand macro="requirements"> |
7 <requirement type="package" version="0.24.2">pandas</requirement> | 7 <requirement type="package" version="0.25.1">pandas</requirement> |
8 </expand> | 8 </expand> |
9 <command detect_errors="exit_code"> | 9 <command detect_errors="exit_code"> |
10 <![CDATA[ | 10 <![CDATA[ |
11 python '$__tool_directory__/hbonds.py' | 11 python '$__tool_directory__/hbonds.py' |
12 --idcd '$dcdin' | 12 --itraj '$trajin' |
13 --ipdb '$pdbin' | 13 --istr '$strin' |
14 --itrajext '$trajin.ext' | |
15 --istrext '$strin.ext' | |
14 --isegid1 '$segid1' | 16 --isegid1 '$segid1' |
15 --isegid2 '$segid2' | 17 --isegid2 '$segid2' |
16 --idistance '$distance' | 18 --idistance '$distance' |
17 --iangle '$angle' | 19 --iangle '$angle' |
18 --output '$output' | 20 --output '$output' |
21 --otime_output '$time_output' | 23 --otime_output '$time_output' |
22 2>&1 | 24 2>&1 |
23 ]]></command> | 25 ]]></command> |
24 <inputs> | 26 <inputs> |
25 <expand macro="analysis_inputs"/> | 27 <expand macro="analysis_inputs"/> |
26 <param name="segid1" type="text" value="PRO" label="Segid of selection 1"/> | 28 <param name="segid1" type="text" value="PRO" label="Segment ID of selection 1"/> |
27 <param name="segid2" type="text" value="HET" label="Segid of selection 2"/> | 29 <param name="segid2" type="text" value="HET" label="Segment ID of selection 2"/> |
28 <param name="distance" type="float" value="3.0" label="Cutoff distance"/> | 30 <param name="distance" type="float" value="3.0" label="Cutoff distance"/> |
29 <param name="angle" type="float" value="120.0" label="Cutoff angle"/> | 31 <param name="angle" type="float" value="120.0" label="Cutoff angle"/> |
30 </inputs> | 32 </inputs> |
31 <outputs> | 33 <outputs> |
32 <data format="tabular" name="output" label="Hbond Analysis raw data"/> | 34 <data format="tabular" name="output" label="H-bond analysis raw data"/> |
33 <data format="tabular" name="freq_output" label="Hbond Frequency"/> | 35 <data format="tabular" name="freq_output" label="H-bond frequency"/> |
34 <data format="tabular" name="number_output" label="Number of Hbonds Per Time Step"/> | 36 <data format="tabular" name="number_output" label="Number of H-bonds per time step"/> |
35 <data format="tabular" name="time_output" label="Time Steps for Each Observed Hbond"/> | 37 <data format="tabular" name="time_output" label="Time steps for each observed H-bond"/> |
36 </outputs> | 38 </outputs> |
37 <tests> | 39 <tests> |
38 <test> | 40 <test> |
39 <expand macro="tests_inputs"/> | 41 <expand macro="tests_inputs"/> |
40 <param name="distance" value="3.0"/> | 42 <param name="distance" value="3.0"/> |
49 <help><![CDATA[ | 51 <help><![CDATA[ |
50 .. class:: infomark | 52 .. class:: infomark |
51 | 53 |
52 **What it does** | 54 **What it does** |
53 | 55 |
54 This tool calculates hydrogen bonds between two segments of the system. | 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. |
55 | 57 |
56 _____ | 58 _____ |
57 | 59 |
58 | 60 |
59 .. class:: infomark | 61 .. class:: infomark |
60 | 62 |
61 **Input** | 63 **Input** |
62 | 64 |
63 - Trajectory file (DCD). | 65 - Trajectory file (DCD). |
64 - PDB file. | 66 - PDB file. |
65 - Segids of the two segments. | 67 - Segment IDs of the two segments. |
66 - cutoff distance and angle. | 68 - Cutoff distance and angle. |
67 | 69 |
68 _____ | 70 _____ |
69 | 71 |
70 | 72 |
71 .. class:: infomark | 73 .. class:: infomark |
72 | 74 |
73 **Output** | 75 **Output** |
74 | 76 |
75 - .csv files of the Hbond frequency, number of Hbonds Per time step, and time steps for each observed Hbond | 77 - Tabular files containing H-bond frequency, number of H-bonds Per time step, and time steps for each observed H-bond. |
76 | 78 |
77 | 79 |
78 ]]></help> | 80 ]]></help> |
79 <expand macro="citations" /> | 81 <expand macro="citations" /> |
80 </tool> | 82 </tool> |