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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
author chemteam
date Wed, 03 Apr 2019 15:40:31 -0400
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-1:000000000000 0:f739a9e4ed06
1 <tool id="mdanalysis_ramachandran_plot" name="Ramachandran Plots" version="0.1.3">
2 <description>Calculate and plot the distribution of two diheadrals in a trajectory</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements">
7 <requirement type="package" version="1.2.1">scipy</requirement>
8 <requirement type="package" version="0.9.0">seaborn</requirement>
9 <requirement type="package" version="1.0.5">nbdime</requirement>
10 </expand>
11 <command detect_errors="exit_code">
12 <![CDATA[
13 python '$__tool_directory__/ramachandran_plots.py'
14 --idcd '$dcdin'
15 --ipdb '$pdbin'
16 --isegid1 '$phi.segid1'
17 --iresid1 '$phi.resid1'
18 --iname1 '$phi.name1'
19 --isegid2 '$phi.segid2'
20 --iresid2 '$phi.resid2'
21 --iname2 '$phi.name2'
22 --isegid3 '$phi.segid3'
23 --iresid3 '$phi.resid3'
24 --iname3 '$phi.name3'
25 --isegid4 '$phi.segid4'
26 --iresid4 '$phi.resid4'
27 --iname4 '$phi.name4'
28 --isegid5 '$psi.segid1'
29 --iresid5 '$psi.resid1'
30 --iname5 '$psi.name1'
31 --isegid6 '$psi.segid2'
32 --iresid6 '$psi.resid2'
33 --iname6 '$psi.name2'
34 --isegid7 '$psi.segid3'
35 --iresid7 '$psi.resid3'
36 --iname7 '$psi.name3'
37 --isegid8 '$psi.segid4'
38 --iresid8 '$psi.resid4'
39 --iname8 '$psi.name4'
40 --output '$output'
41 --oramachandran_plot '$ramachandran_plot'
42 2>&1
43 ]]></command>
44 <inputs>
45 <expand macro="analysis_inputs"/>
46 <section name="phi" title="Phi" expanded="False">
47 <param name="segid1" type="text" value="HET" label="Segid of atom 1">
48 <expand macro="sanitizer"/>
49 </param>
50 <param name="resid1" type="text" value="3" label="Resid of atom 1">
51 <expand macro="sanitizer_resids"/>
52 </param>
53 <param name="name1" type="text" value="O5" label="Atom name of atom 1">
54 <expand macro="sanitizer"/>
55 </param>
56 <param name="segid2" type="text" value="HET" label="Segid of atom 2">
57 <expand macro="sanitizer"/>
58 </param>
59 <param name="resid2" type="text" value="3" label="Resid of atom 2">
60 <expand macro="sanitizer_resids"/>
61 </param>
62 <param name="name2" type="text" value="C1" label="Atom name of atom 2">
63 <expand macro="sanitizer"/>
64 </param>
65 <param name="segid3" type="text" value="HET" label="Segid of atom 3">
66 <expand macro="sanitizer"/>
67 </param>
68 <param name="resid3" type="text" value="2" label="Resid of atom 3">
69 <expand macro="sanitizer_resids"/>
70 </param>
71 <param name="name3" type="text" value="O4" label="Atom name of atom 3">
72 <expand macro="sanitizer"/>
73 </param>
74 <param name="segid4" type="text" value="HET" label="Segid of atom 4">
75 <expand macro="sanitizer"/>
76 </param>
77 <param name="resid4" type="text" value="2" label="Resid of atom 4">
78 <expand macro="sanitizer_resids"/>
79 </param>
80 <param name="name4" type="text" value="C4" label="Atom name of atom 4">
81 <expand macro="sanitizer"/>
82 </param>
83 </section>
84 <section name="psi" title="Psi" expanded="False">
85 <param name="segid1" type="text" value="HET" label="Segid of atom 1">
86 <expand macro="sanitizer"/>
87 </param>
88 <param name="resid1" type="text" value="3" label="Resid of atom 1">
89 <expand macro="sanitizer_resids"/>
90 </param>
91 <param name="name1" type="text" value="C1" label="Atom name of atom 1">
92 <expand macro="sanitizer"/>
93 </param>
94 <param name="segid2" type="text" value="HET" label="Segid of atom 2">
95 <expand macro="sanitizer"/>
96 </param>
97 <param name="resid2" type="text" value="2" label="Resid of atom 2">
98 <expand macro="sanitizer_resids"/>
99 </param>
100 <param name="name2" type="text" value="O4" label="Atom name of atom 2">
101 <expand macro="sanitizer"/>
102 </param>
103 <param name="segid3" type="text" value="HET" label="Segid of atom 3">
104 <expand macro="sanitizer"/>
105 </param>
106 <param name="resid3" type="text" value="2" label="Resid of atom 3">
107 <expand macro="sanitizer_resids"/>
108 </param>
109 <param name="name3" type="text" value="C4" label="Atom name of atom 3">
110 <expand macro="sanitizer"/>
111 </param>
112 <param name="segid4" type="text" value="HET" label="Segid of atom 4">
113 <expand macro="sanitizer"/>
114 </param>
115 <param name="resid4" type="text" value="2" label="Resid of atom 4">
116 <expand macro="sanitizer_resids"/>
117 </param>
118 <param name="name4" type="text" value="C3" label="Atom name of atom 4">
119 <expand macro="sanitizer"/>
120 </param>
121 </section>
122 </inputs>
123 <outputs>
124 <data format="tabular" name="output" label="Ramachandran Plot raw data"/>
125 <data format="png" name="ramachandran_plot" label="Ramachandran Plot"/>
126 </outputs>
127 <tests>
128 <test>
129 <expand macro="tests_inputs"/>
130 <param name="phi.segid1" value="HET"/>
131 <param name="phi.resid1" value="3"/>
132 <param name="phi.name1" value="O5"/>
133 <param name="phi.segid2" value="HET"/>
134 <param name="phi.resid2" value="3"/>
135 <param name="phi.name2" value="C1"/>
136 <param name="phi.segid3" value="HET"/>
137 <param name="phi.resid3" value="2"/>
138 <param name="phi.name3" value="O4"/>
139 <param name="phi.segid4" value="HET"/>
140 <param name="phi.resid4" value="2"/>
141 <param name="phi.name4" value="C4"/>
142 <param name="psi.segid1" value="HET"/>
143 <param name="psi.resid1" value="3"/>
144 <param name="psi.name1" value="C1"/>
145 <param name="psi.segid2" value="HET"/>
146 <param name="psi.resid2" value="2"/>
147 <param name="psi.name2" value="O4"/>
148 <param name="psi.segid3" value="HET"/>
149 <param name="psi.resid3" value="2"/>
150 <param name="psi.name3" value="C4"/>
151 <param name="psi.segid4" value="HET"/>
152 <param name="psi.resid4" value="2"/>
153 <param name="psi.name4" value="C3"/>
154 <output name="output" file="Ramachandran_Plot_raw_data.tabular" />
155 </test>
156 </tests>
157 <help><![CDATA[
158 .. class:: infomark
159
160 **What it does**
161
162 A Ramachandran plot ([φ,ψ] plot), originally developed as a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid.
163 This can be also used to calculate glycosidic φ and ψ angles formed between carbohydrates. This tool can calculate and plot the histogram (ramachandran plot) of user define φ and ψ angles of a trajectory.
164
165 - For protien φ and ψ diheadral definitions see https://proteinstructures.com/Structure/Structure/Ramachandran-plot.html.
166
167 - For glycan φ and ψ diheadral definitions see http://www.glycanstructure.org/
168
169 _____
170
171
172 .. class:: infomark
173
174 **Input**
175
176 - Trajectory file (DCD).
177 - PDB file.
178 - Segids, resids and names of the four atoms to calculate diheadrals.
179
180 _____
181
182
183 .. class:: infomark
184
185 **Output**
186
187 - Tab-separated file of raw data of the φ,ψ angles time series.
188 - Image (as png) of the Ramachandran Plot.
189
190
191 ]]></help>
192 <expand macro="citations" />
193 </tool>