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comparison pca.xml @ 5:24867ab16f36 draft default tip

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:45:05 -0400
parents 54dd1596e04e
children
comparison
equal deleted inserted replaced
4:994c509873db 5:24867ab16f36
1 <tool id="bio3d_pca" name="PCA" version="@VERSION@"> 1 <tool id="bio3d_pca" name="PCA" version="@VERSION@">
2 <description>Principle component analysis using Bio3D</description> 2 <description>- principal component analysis using Bio3D</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code">
60 <expand macro="analysis_inputs"/> 60 <expand macro="analysis_inputs"/>
61 <param name="method" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" 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" /> 62 label="Use singular value decomposition (SVD) instead of default eigenvalue decomposition ?" help="Default: No" />
63 <conditional name="pca"> 63 <conditional name="pca">
64 <param name="sele" type="select" label="Select domains"> 64 <param name="sele" type="select" label="Select domains">
65 <option value="calpha">Calpha</option> 65 <option value="calpha">C-alpha</option>
66 <option value="cbeta">Cbeta</option> 66 <option value="cbeta">C-beta</option>
67 <option value="backbone">Backbone</option> 67 <option value="backbone">Backbone</option>
68 <option value="sidechain">Sidechain</option> 68 <option value="sidechain">Sidechain</option>
69 <option value="protein">Protein</option> 69 <option value="protein">Protein</option>
70 <option value="ligand">Ligand</option> 70 <option value="ligand">Ligand</option>
71 <option value="nucleic">Nucleic Acids</option> 71 <option value="nucleic">Nucleic acids</option>
72 <option value="elety">Atom Names</option> 72 <option value="elety">Atom names</option>
73 <option value="resid">Resid</option> 73 <option value="resid">Residue ID</option>
74 <option value="segid">Segid</option> 74 <option value="segid">Segment ID</option>
75 </param> 75 </param>
76 <when value="calpha"> 76 <when value="calpha">
77 </when> 77 </when>
78 <when value="cbeta"> 78 <when value="cbeta">
79 </when> 79 </when>
86 <when value="ligand"> 86 <when value="ligand">
87 </when> 87 </when>
88 <when value="nucleic"> 88 <when value="nucleic">
89 </when> 89 </when>
90 <when value="elety"> 90 <when value="elety">
91 <param name="elety" type="text" value="CA" label="Atom Name"/> 91 <param name="elety" type="text" value="CA" label="Atom name"/>
92 </when> 92 </when>
93 <when value="resid"> 93 <when value="resid">
94 <param name="resid" type="text" value="BGLC" label="Resid"/> 94 <param name="resid" type="text" value="BGLC" label="Residue ID"/>
95 </when> 95 </when>
96 <when value="segid"> 96 <when value="segid">
97 <param name="segid" type="text" value="SUBS" label="Segid"/> 97 <param name="segid" type="text" value="SUBS" label="Segment ID"/>
98 </when> 98 </when>
99 </conditional> 99 </conditional>
100 </inputs> 100 </inputs>
101 <outputs> 101 <outputs>
102 <data format="tabular" name="output" label="PCA raw data"/> 102 <data format="tabular" name="output" label="PCA raw data"/>
120 <help><![CDATA[ 120 <help><![CDATA[
121 .. class:: infomark 121 .. class:: infomark
122 122
123 **What it does** 123 **What it does**
124 124
125 PCA can be used to determine the relationship between statistically meaningful conformations (major global motions) 125 Principal component analysis (PCA) can be used to determine the relationship between statistically meaningful conformations (major global motions)
126 sampled during the trajectory. 126 sampled during the trajectory.
127 127
128 _____ 128 _____
129 129
130 130
131 .. class:: infomark 131 .. class:: infomark
132 132
133 **Input** 133 **Input**
134 134
135 - Input file in PDB format 135 - Input file in PDB format
136 - Input file in dcd format 136 - Input file in DCD format
137 137
138 _____ 138 _____
139 139
140 140
141 .. class:: infomark 141 .. class:: infomark
142 142
143 **Output** 143 **Output**
144 144
145 - Image (as PNG) of the pca plot 145 - Image (as PNG) of the PCA plot
146 - Image (as PNG) of the pca clusterd plot 146 - Image (as PNG) of the PCA clustered plot
147 - Image (as PNG) of the PC1 plotted on RMSF 147 - Image (as PNG) of the first principal component plotted on RMSF
148 - Tab-separated file of raw data 148 - Tab-separated file of raw data
149 149
150 ]]></help> 150 ]]></help>
151 <expand macro="citations" /> 151 <expand macro="citations" />
152 </tool> 152 </tool>