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comparison pca.xml @ 0:f56fb2762abb draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 580d80c3fd856bb3ae18ef7b5458eb3b5e2c7374
author chemteam
date Mon, 08 Oct 2018 12:49:36 -0400
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children 54dd1596e04e
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-1:000000000000 0:f56fb2762abb
1 <tool id="bio3d_pca" name="PCA" version="@VERSION@">
2 <description>Principle component analysis using Bio3D</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code">
8 <![CDATA[
9 Rscript '$__tool_directory__/pca.R'
10 '$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 '$output'
54 '$pca_plot'
55 '$pca_cluster'
56 '$pc1_rmsf'
57 2>&1
58 ]]></command>
59 <inputs>
60 <expand macro="analysis_inputs"/>
61 <param name="method" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
62 label="Use singular value decomposition (SVD) instead of default eigenvalue decomposition ?" help="Default: No" />
63 <conditional name="pca">
64 <param name="sele" type="select" label="Select domains">
65 <option value="calpha">Calpha</option>
66 <option value="cbeta">Cbeta</option>
67 <option value="backbone">Backbone</option>
68 <option value="sidechain">Sidechain</option>
69 <option value="protein">Protein</option>
70 <option value="ligand">Ligand</option>
71 <option value="nucleic">Nucleic Acids</option>
72 <option value="elety">Atom Names</option>
73 <option value="resid">Resid</option>
74 <option value="segid">Segid</option>
75 </param>
76 <when value="calpha">
77 </when>
78 <when value="cbeta">
79 </when>
80 <when value="backbone">
81 </when>
82 <when value="sidechain">
83 </when>
84 <when value="protein">
85 </when>
86 <when value="ligand">
87 </when>
88 <when value="nucleic">
89 </when>
90 <when value="elety">
91 <param name="elety" type="text" value="CA" label="Atom Name"/>
92 </when>
93 <when value="resid">
94 <param name="resid" type="text" value="BGLC" label="Resid"/>
95 </when>
96 <when value="segid">
97 <param name="segid" type="text" value="SUBS" label="Segid"/>
98 </when>
99 </conditional>
100 </inputs>
101 <outputs>
102 <data format="tabular" name="output" label="PCA raw data"/>
103 <data format="png" name="pca_plot" label="PCA plot"/>
104 <data format="png" name="pca_cluster" label="PCA Cluster Plot"/>
105 <data format="png" name="pc1_rmsf" label="PC1 on RMSF"/>
106 </outputs>
107 <tests>
108 <test>
109 <expand macro="tests_inputs"/>
110 <param name="method" value="false"/>
111 <param name="sele" value="calpha"/>
112 <output name="output">
113 <assert_contents>
114 <has_n_columns n="4" />
115 </assert_contents>
116 </output>
117 </test>
118 </tests>
119 <help><![CDATA[
120 .. class:: infomark
121
122 **What it does**
123
124 PCA can be used to determine the relationship between statistically meaningful conformations (major global motions)
125 sampled during the trajectory.
126
127 _____
128
129
130 .. class:: infomark
131
132 **Input**
133
134 - Input file in PDB format
135 - Input file in dcd format
136
137 _____
138
139
140 .. class:: infomark
141
142 **Output**
143
144 - Image (as PNG) of the pca plot
145 - Image (as PNG) of the pca clusterd plot
146 - Image (as PNG) of the PC1 plotted on RMSF
147 - Tab-separated file of raw data
148
149 ]]></help>
150 <expand macro="citations" />
151 </tool>