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comparison hbonds.xml @ 1:525e4dd613fc draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:40:53 -0400
parents bad21f113679
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0:bad21f113679 1:525e4dd613fc
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>