Mercurial > repos > chemteam > mdanalysis_dihedral

comparison dihedrals.xml @ 4:d8178fe9aaff 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 12:52:20 -0400
parents 2fff8653412f
children aaa130695a2b
comparison
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3:554f60da9c8f 4:d8178fe9aaff
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 '$__tool_directory__/dihedrals.py' 9 python '$__tool_directory__/dihedrals.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'
25 --odihedral_plot '$dihedral_plot' 27 --odihedral_plot '$dihedral_plot'
26 2>&1 28 2>&1
27 ]]></command> 29 ]]></command>
28 <inputs> 30 <inputs>
29 <expand macro="analysis_inputs"/> 31 <expand macro="analysis_inputs"/>
30 <param name="segid1" type="text" value="PRO" label="Segid of atom 1"/> 32 <param name="segid1" type="text" value="PRO" label="Segment ID of atom 1"/>
31 <param name="resid1" type="text" value="212" label="Resid of atom 1"/> 33 <param name="resid1" type="text" value="212" label="Residue ID of atom 1"/>
32 <param name="name1" type="text" value="OE2" label="Atom name of atom 1"/> 34 <param name="name1" type="text" value="OE2" label="Atom name of atom 1"/>
33 <param name="segid2" type="text" value="HET" label="Segid of atom 2"/> 35 <param name="segid2" type="text" value="HET" label="Segment ID of atom 2"/>
34 <param name="resid2" type="text" value="3" label="Resid of atom 2"/> 36 <param name="resid2" type="text" value="3" label="Residue ID of atom 2"/>
35 <param name="name2" type="text" value="C1" label="Atom name of atom 2"/> 37 <param name="name2" type="text" value="C1" label="Atom name of atom 2"/>
36 <param name="segid3" type="text" value="HET" label="Segid of atom 3"/> 38 <param name="segid3" type="text" value="HET" label="Segment ID of atom 3"/>
37 <param name="resid3" type="text" value="3" label="Resid of atom 3"/> 39 <param name="resid3" type="text" value="3" label="Residue ID of atom 3"/>
38 <param name="name3" type="text" value="C2" label="Atom name of atom 3"/> 40 <param name="name3" type="text" value="C2" label="Atom name of atom 3"/>
39 <param name="segid4" type="text" value="HET" label="Segid of atom 4"/> 41 <param name="segid4" type="text" value="HET" label="Segment ID of atom 4"/>
40 <param name="resid4" type="text" value="3" label="Resid of atom 4"/> 42 <param name="resid4" type="text" value="3" label="Residue ID of atom 4"/>
41 <param name="name4" type="text" value="C3" label="Atom name of atom 4"/> 43 <param name="name4" type="text" value="C3" label="Atom name of atom 4"/>
42 </inputs> 44 </inputs>
43 <outputs> 45 <outputs>
44 <data format="tabular" name="output" label="Dihedral analysis raw data"/> 46 <data format="tabular" name="output" label="Dihedral analysis raw data"/>
45 <data format="png" name="dihedral_plot" label="Dihedral Analysis Plot"/> 47 <data format="png" name="dihedral_plot" label="Dihedral analysis plot"/>
46 </outputs> 48 </outputs>
47 <tests> 49 <tests>
48 <test> 50 <test>
49 <expand macro="tests_inputs"/> 51 <expand macro="tests_inputs"/>
50 <param name="segid1" value="PRO"/> 52 <param name="segid1" value="PRO"/>
59 <param name="segid4" value="HET"/> 61 <param name="segid4" value="HET"/>
60 <param name="resid4" value="3"/> 62 <param name="resid4" value="3"/>
61 <param name="name4" value="C3"/> 63 <param name="name4" value="C3"/>
62 <output name="output" file="Dihedral_analysis_raw_data.tabular" /> 64 <output name="output" file="Dihedral_analysis_raw_data.tabular" />
63 </test> 65 </test>
66 <test>
67 <expand macro="tests_inputs_gmx"/>
68 <param name="segid1" value="SYSTEM"/>
69 <param name="resid1" value="212"/>
70 <param name="name1" value="OE2"/>
71 <param name="segid2" value="SYSTEM"/>
72 <param name="resid2" value="3"/>
73 <param name="name2" value="C1"/>
74 <param name="segid3" value="SYSTEM"/>
75 <param name="resid3" value="3"/>
76 <param name="name3" value="C2"/>
77 <param name="segid4" value="SYSTEM"/>
78 <param name="resid4" value="3"/>
79 <param name="name4" value="C3"/>
80 <output name="output">
81 <assert_contents>
82 <has_n_columns n="2" />
83 <has_line_matching expression="0\t-61.*" />
84 <has_line_matching expression="12\t-76.*" />
85 <has_line_matching expression="4\t-66.*" />
86 </assert_contents>
87 </output>
88 </test>
64 </tests> 89 </tests>
65 <help><![CDATA[ 90 <help><![CDATA[
66 .. class:: infomark 91 .. class:: infomark
67 92
68 **What it does** 93 **What it does**
76 101
77 **Input** 102 **Input**
78 103
79 - Trajectory file (DCD). 104 - Trajectory file (DCD).
80 - PDB file. 105 - PDB file.
81 - Segids, resids and names of the four atoms to calculate dihedral angle. 106 - Segment IDs, residue IDs and names of the four atoms to calculate the dihedral angle.
82 107
108 Note that a MDAnalysis 'segment' is a larger organizational unit, for example one protein or all the solvent molecules or simply the whole system.
109
83 _____ 110 _____
84 111
85 112
86 .. class:: infomark 113 .. class:: infomark
87 114
88 **Output** 115 **Output**
89 116
90 - Tab-separated file of raw data of the dihedral angle between two intersecting planes calculated for each frame. 117 - Tab-separated file of raw data of the dihedral angle calculated for each frame.
91 - Image (as png) of the time series graph. 118 - Image (as png) of the time series graph.
92 119
93 ]]></help> 120 ]]></help>
94 <expand macro="citations" /> 121 <expand macro="citations" />
95 </tool> 122 </tool>