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comparison angle.xml @ 4:8a5c112aa0f1 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 12:40:22 -0400
parents 72aaaa34dda5
children
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3:c19dea167308 4:8a5c112aa0f1
1 <tool id="mdanalysis_angle" name="Angle Analysis" version="@VERSION@"> 1 <tool id="mdanalysis_angle" name="Angle Analysis" version="@VERSION@">
2 <description>Time series of Angles</description> 2 <description>- time series of Angles</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 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code">
8 <![CDATA[ 8 <![CDATA[
9 python '$__tool_directory__/angle.py' 9 python '$__tool_directory__/angle.py'
10 --idcd '$dcdin' 10 --itraj '$trajin'
11 --ipdb '$pdbin' 11 --istr '$strin'
12 --itrajext '$trajin.ext'
13 --istrext '$strin.ext'
12 --isegid1 '$segid1' 14 --isegid1 '$segid1'
13 --iresid1 '$resid1' 15 --iresid1 '$resid1'
14 --iname1 '$name1' 16 --iname1 '$name1'
15 --isegid2 '$segid2' 17 --isegid2 '$segid2'
16 --iresid2 '$resid2' 18 --iresid2 '$resid2'
22 --oangle_plot '$angle_plot' 24 --oangle_plot '$angle_plot'
23 2>&1 25 2>&1
24 ]]></command> 26 ]]></command>
25 <inputs> 27 <inputs>
26 <expand macro="analysis_inputs"/> 28 <expand macro="analysis_inputs"/>
27 <param name="segid1" type="text" value="PRO" label="Segid of atom 1"/> 29 <param name="segid1" type="text" value="PRO" label="Segment ID of atom 1"/>
28 <param name="resid1" type="text" value="212" label="Resid of atom 1"/> 30 <param name="resid1" type="text" value="212" label="Residue ID of atom 1"/>
29 <param name="name1" type="text" value="OE2" label="Atom name of atom 1"/> 31 <param name="name1" type="text" value="OE2" label="Atom name of atom 1"/>
30 <param name="segid2" type="text" value="HET" label="Segid of atom 2"/> 32 <param name="segid2" type="text" value="HET" label="Segment ID of atom 2"/>
31 <param name="resid2" type="text" value="3" label="Resid of atom 2"/> 33 <param name="resid2" type="text" value="3" label="Residue ID of atom 2"/>
32 <param name="name2" type="text" value="C1" label="Atom name of atom 2"/> 34 <param name="name2" type="text" value="C1" label="Atom name of atom 2"/>
33 <param name="segid3" type="text" value="HET" label="Segid of atom 3"/> 35 <param name="segid3" type="text" value="HET" label="Segment ID of atom 3"/>
34 <param name="resid3" type="text" value="3" label="Resid of atom 3"/> 36 <param name="resid3" type="text" value="3" label="Residue ID of atom 3"/>
35 <param name="name3" type="text" value="C2" label="Atom name of atom 3"/> 37 <param name="name3" type="text" value="C2" label="Atom name of atom 3"/>
36 </inputs> 38 </inputs>
37 <outputs> 39 <outputs>
38 <data format="tabular" name="output" label="Angle Analysis raw data"/> 40 <data format="tabular" name="output" label="Angle Analysis raw data"/>
39 <data format="png" name="angle_plot" label="Angle Analysis Plot"/> 41 <data format="png" name="angle_plot" label="Angle Analysis Plot"/>
50 <param name="segid3" value="HET"/> 52 <param name="segid3" value="HET"/>
51 <param name="resid3" value="3"/> 53 <param name="resid3" value="3"/>
52 <param name="name3" value="C2"/> 54 <param name="name3" value="C2"/>
53 <output name="output" file="Angle_Analysis_raw_data.tabular" /> 55 <output name="output" file="Angle_Analysis_raw_data.tabular" />
54 </test> 56 </test>
57 <test>
58 <expand macro="tests_inputs_gmx"/>
59 <param name="segid1" value="SYSTEM"/>
60 <param name="resid1" value="212"/>
61 <param name="name1" value="OE2"/>
62 <param name="segid2" value="SYSTEM"/>
63 <param name="resid2" value="3"/>
64 <param name="name2" value="C1"/>
65 <param name="segid3" value="SYSTEM"/>
66 <param name="resid3" value="3"/>
67 <param name="name3" value="C2"/>
68 <output name="output">
69 <assert_contents>
70 <has_n_columns n="2" />
71 <has_line_matching expression="0.0\t70.*" />
72 <has_line_matching expression="10.0\t71.*" />
73 <has_line_matching expression="11.0\t81.*" />
74 </assert_contents>
75 </output>
76 </test>
55 </tests> 77 </tests>
56 <help><![CDATA[ 78 <help><![CDATA[
57 .. class:: infomark 79 .. class:: infomark
58 80
59 **What it does** 81 **What it does**
60 82
61 This tool calculates and plot angle between three atoms. 83 This tool calculates and plots the angle between three atoms.
62 84
63 _____ 85 _____
64 86
65 87
66 .. class:: infomark 88 .. class:: infomark
67 89
68 **Input** 90 **Input**
69 91
70 - Trajectory file (DCD). 92 - Trajectory file (DCD).
71 - PDB file. 93 - PDB file.
72 - Segids, resids and names of the three atoms to calculate angles. 94 - Segment IDs, residue IDs and names of the three atoms for calculating angles.
73 95
96 Note that a MDAnalysis 'segment' is a larger organizational unit, for example one protein or all the solvent molecules or simply the whole system.
97
74 _____ 98 _____
75 99
76 100
77 .. class:: infomark 101 .. class:: infomark
78 102
79 **Output** 103 **Output**
80 104
81 - Tab-separated file of raw data of angle between three atoms calculated for each frame. 105 - Tab-separated file of raw data of the angle between three atoms calculated for each frame.
82 - Image (as png) of the time series graph. 106 - Image (as png) of the time series graph.
83
84 107
85 ]]></help> 108 ]]></help>
86 <expand macro="citations" /> 109 <expand macro="citations" />
87 </tool> 110 </tool>