Mercurial > repos > chemteam > bio3d_pca_visualize

comparison visualize_pc.xml @ 0:d16c1aea2333 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit cd0830e5e3502721fa355cc8e3fedc331201a6e4
author chemteam
date Tue, 26 Feb 2019 08:26:54 -0500
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children eebc574b0923
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-1:000000000000 0:d16c1aea2333
1 <tool id="bio3d_pca_visualize" name="PCA visualization" version="@VERSION@">
2 <description>Generate trajectories of principle components of motions</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code">
8 <![CDATA[
9 Rscript '$__tool_directory__/visualize_pc.R'
10 '$dcdin'
11 '$pdbin'
12 '$method'
13 #if $pca.sele == 'calpha':
14 "string"
15 "calpha"
16 #end if
17 #if $pca.sele == 'cbeta':
18 "string"
19 '$pca.cbeta'
20 #end if
21 #if $pca.sele == 'backbone':
22 "string"
23 "backbone"
24 #end if
25 #if $pca.sele == 'sidechain':
26 "string"
27 "sidechain"
28 #end if
29 #if $pca.sele == 'protein':
30 "string"
31 "protein"
32 #end if
33 #if $pca.sele == 'ligand':
34 "string"
35 "ligand"
36 #end if
37 #if $pca.sele == 'nucleic':
38 "string"
39 "nucleic"
40 #end if
41 #if $pca.sele == 'elety':
42 "elety"
43 '$pca.elety'
44 #end if
45 #if $pca.sele == 'resid':
46 "resid"
47 '$pca.resid'
48 #end if
49 #if $pca.sele == 'segid':
50 "segid"
51 '$pca.segid'
52 #end if
53 '$pc_id'
54 '$pdbout'
55 2>&1
56 ]]></command>
57 <inputs>
58 <expand macro="analysis_inputs"/>
59 <param name="method" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
60 label="Use singular value decomposition (SVD) instead of default eigenvalue decomposition ?" help="Default: No" />
61 <conditional name="pca">
62 <param name="sele" type="select" label="Select domains">
63 <option value="calpha">Calpha</option>
64 <option value="cbeta">Cbeta</option>
65 <option value="backbone">Backbone</option>
66 <option value="sidechain">Sidechain</option>
67 <option value="protein">Protein</option>
68 <option value="ligand">Ligand</option>
69 <option value="nucleic">Nucleic Acids</option>
70 <option value="elety">Atom Names</option>
71 <option value="resid">Resid</option>
72 <option value="segid">Segid</option>
73 </param>
74 <when value="calpha"/>
75 <when value="cbeta"/>
76 <when value="backbone"/>
77 <when value="sidechain"/>
78 <when value="protein"/>
79 <when value="ligand"/>
80 <when value="nucleic"/>
81 <when value="elety">
82 <param name="elety" type="text" value="CA" label="Atom Name"/>
83 </when>
84 <when value="resid">
85 <param name="resid" type="text" value="BGLC" label="Resid"/>
86 </when>
87 <when value="segid">
88 <param name="segid" type="text" value="SUBS" label="Segid"/>
89 </when>
90 </conditional>
91 <param name="pc_id" type="integer" value="1" label="Principle component id"/>
92 </inputs>
93 <outputs>
94 <data format="pdb" name="pdbout" label="PCA_${pc_id}.pdb"/>
95 </outputs>
96 <tests>
97 <test>
98 <expand macro="tests_inputs"/>
99 <param name="method" value="false"/>
100 <param name="sele" value="calpha"/>
101 <param name="pc_id" value="1"/>
102 <output name="pdbout" file="PCA_1.pdb" />
103 </test>
104 </tests>
105 <help><![CDATA[
106 .. class:: infomark
107
108 **What it does**
109
110 This tool can generate small trajectories of a given principle component.
111
112 _____
113
114
115 .. class:: infomark
116
117 **Input**
118
119 - Input file in PDB format
120 - Input file in dcd format
121
122 _____
123
124
125 .. class:: infomark
126
127 **Output**
128
129 - A short trajectory (as PDB) of the given priciple component id.
130
131
132 ]]></help>
133 <expand macro="citations" />
134 </tool>