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comparison dihedrals.xml @ 0:f95d4348ed7c draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
author chemteam
date Mon, 08 Oct 2018 13:16:46 -0400
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-1:000000000000 0:f95d4348ed7c
1 <tool id="mdanalysis_dihedral" name="Dihedral Analysis" version="@VERSION@">
2 <description>Time series of dihedrals</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code">
8 <![CDATA[
9 python '$__tool_directory__/dihedrals.py'
10 --idcd '$dcdin'
11 --ipdb '$pdbin'
12 --isegid1 '$segid1'
13 --iresid1 '$resid1'
14 --iname1 '$name1'
15 --isegid2 '$segid2'
16 --iresid2 '$resid2'
17 --iname2 '$name2'
18 --isegid3 '$segid3'
19 --iresid3 '$resid3'
20 --iname3 '$name3'
21 --isegid4 '$segid4'
22 --iresid4 '$resid4'
23 --iname4 '$name4'
24 --output '$output'
25 --odihedral_plot '$dihedral_plot'
26 2>&1
27 ]]></command>
28 <inputs>
29 <expand macro="analysis_inputs"/>
30 <param name="segid1" type="text" value="PRO" label="Segid of atom 1"/>
31 <param name="resid1" type="text" value="212" label="Resid of atom 1"/>
32 <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"/>
34 <param name="resid2" type="text" value="3" label="Resid of atom 2"/>
35 <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"/>
37 <param name="resid3" type="text" value="3" label="Resid of atom 3"/>
38 <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"/>
40 <param name="resid4" type="text" value="3" label="Resid of atom 4"/>
41 <param name="name4" type="text" value="C3" label="Atom name of atom 4"/>
42 </inputs>
43 <outputs>
44 <data format="tabular" name="output" label="Dihedral analysis raw data"/>
45 <data format="png" name="dihedral_plot" label="Dihedral Analysis Plot"/>
46 </outputs>
47 <tests>
48 <test>
49 <expand macro="tests_inputs"/>
50 <param name="segid1" value="PRO"/>
51 <param name="resid1" value="212"/>
52 <param name="name1" value="OE2"/>
53 <param name="segid2" value="HET"/>
54 <param name="resid2" value="3"/>
55 <param name="name2" value="C1"/>
56 <param name="segid3" value="HET"/>
57 <param name="resid3" value="3"/>
58 <param name="name3" value="C2"/>
59 <param name="segid3" value="HET"/>
60 <param name="resid3" value="3"/>
61 <param name="name3" value="C3"/>
62 <output name="output">
63 <assert_contents>
64 <has_n_columns n="2" />
65 </assert_contents>
66 </output>
67 </test>
68 </tests>
69 <help><![CDATA[
70 .. class:: infomark
71
72 **What it does**
73
74 This tool calculates and plots dihedral angles (angle between two intersecting planes) between four atoms.
75
76 _____
77
78
79 .. class:: infomark
80
81 **Input**
82
83 - Trajectory file (DCD).
84 - PDB file.
85 - Segids, resids and names of the four atoms to calculate dihedral angle.
86
87 _____
88
89
90 .. class:: infomark
91
92 **Output**
93
94 - Tab-separated file of raw data of the dihedral angle between two intersecting planes calculated for each frame.
95 - Image (as png) of the time series graph.
96
97 ]]></help>
98 <expand macro="citations" />
99 </tool>