Mercurial > repos > chemteam > bio3d_dccm
comparison dccm.xml @ 0:386b4f4b6a85 draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 125359d8080653f896089c28cce5308450336f93
author | chemteam |
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date | Wed, 27 Mar 2019 15:16:19 -0400 |
parents | |
children | 18440ff54f63 |
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-1:000000000000 | 0:386b4f4b6a85 |
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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 |