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comparison dccm.xml @ 0:386b4f4b6a85 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
author chemteam
date Wed, 27 Mar 2019 15:16:19 -0400
parents
children 18440ff54f63
comparison
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-1:000000000000 0:386b4f4b6a85
1 <tool id="bio3d_dccm" name="DCCM analysis" version="@VERSION@">
2 <description>Dynamical Cross-Correlation Maps using Bio3D (DCCM)</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code">
8 <![CDATA[
9 Rscript '$__tool_directory__/dccm.R'
10 '$dcdin'
11 '$pdbin'
12 #if $dccm.sele == 'calpha':
13 "string"
14 "calpha"
15 #end if
16 #if $dccm.sele == 'cbeta':
17 "string"
18 '$dccm.cbeta'
19 #end if
20 #if $dccm.sele == 'backbone':
21 "string"
22 "backbone"
23 #end if
24 #if $dccm.sele == 'sidechain':
25 "string"
26 "sidechain"
27 #end if
28 #if $dccm.sele == 'protein':
29 "string"
30 "protein"
31 #end if
32 #if $dccm.sele == 'ligand':
33 "string"
34 "ligand"
35 #end if
36 #if $dccm.sele == 'nucleic':
37 "string"
38 "nucleic"
39 #end if
40 #if $dccm.sele == 'elety':
41 "elety"
42 '$dccm.elety'
43 #end if
44 #if $dccm.sele == 'resid':
45 "resid"
46 '$dccm.resid'
47 #end if
48 #if $dccm.sele == 'segid':
49 "segid"
50 '$dccm.segid'
51 #end if
52 '$output'
53 '$dccm_plot'
54 2>&1
55 ]]></command>
56 <inputs>
57 <expand macro="analysis_inputs"/>
58 <conditional name="dccm">
59 <param name="sele" type="select" label="Select domains">
60 <option value="calpha">Calpha</option>
61 <option value="cbeta">Cbeta</option>
62 <option value="backbone">Backbone</option>
63 <option value="sidechain">Sidechain</option>
64 <option value="protein">Protein</option>
65 <option value="ligand">Ligand</option>
66 <option value="nucleic">Nucleic Acids</option>
67 <option value="elety">Atom Names</option>
68 <option value="resid">Resid</option>
69 <option value="segid">Segid</option>
70 </param>
71 <when value="calpha"/>
72 <when value="cbeta"/>
73 <when value="backbone"/>
74 <when value="sidechain"/>
75 <when value="protein"/>
76 <when value="ligand"/>
77 <when value="nucleic"/>
78 <when value="elety">
79 <param name="elety" type="text" value="CA" label="Atom Name"/>
80 </when>
81 <when value="resid">
82 <param name="resid" type="text" value="BGLC" label="Resid"/>
83 </when>
84 <when value="segid">
85 <param name="segid" type="text" value="SUBS" label="Segid"/>
86 </when>
87 </conditional>
88 </inputs>
89 <outputs>
90 <data format="tabular" name="output" label="DCCM raw data"/>
91 <data format="png" name="dccm_plot" label="DCCM plot"/>
92 </outputs>
93 <tests>
94 <test>
95 <expand macro="tests_inputs"/>
96 <param name="sele" value="calpha"/>
97 <output name="dccm_plot" file="dccm_plot.png" compare="sim_size" delta="20000" />
98 </test>
99 </tests>
100 <help><![CDATA[
101 .. class:: infomark
102
103 **What it does**
104
105 The extent to which the atomic fluctuations/displacements of a system are correlated with one another can be assessed by examining the magnitude of all pairwise cross-correlation coefficients.
106 The DCCM Analysis tool can plot the atom-wise cross-correlations using the Bio3D package. The negative values (negative correlation) indicate the atoms moves in opposite directions and the positive values (positive correlation) indicate the atoms moves in same directions.
107
108 _____
109
110
111 .. class:: infomark
112
113 **Input**
114
115 - Input file in PDB format
116 - Input file in dcd format
117
118 _____
119
120
121 .. class:: infomark
122
123 **Output**
124
125 - Image (as PNG) of the dccm plot
126 - Tab-separated file of raw data
127
128 ]]></help>
129 <expand macro="citations" />
130 </tool>
131