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comparison abims_acp.xml @ 0:79c7fdc90ed6 draft default tip

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author lecorguille
date Tue, 30 Jun 2015 06:38:09 -0400
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1 <tool id="abims_ACP" name="PCA" version="1.2">
2
3 <description>Principal Component Analysis using FactoMineR</description>
4
5 <command interpreter="Rscript">
6 abims_acp.r file "$input" graph TRUE scale.unit "$scale_unit" sep "$sep" dec "$dec"
7 </command>
8
9 <inputs>
10 <param name="input" type="data" label="Data Matrix file" format="tabular" help="Matrix of numeric data with headers." />
11 <!--<param name="graph" type="select" label="graph" help="if FALSE no graph generated">
12 <option value="T" selected="true">TRUE</option>
13 <option value="F" >FALSE</option>
14 </param>-->
15 <param name="scale_unit" type="select" label="scale.unit" help="if FALSE no reduction of variables">
16 <option value="T" selected="true">TRUE</option>
17 <option value="F" >FALSE</option>
18 </param>
19
20 <param name="sep" type="select" format="text" optional="true">
21 <label>Separator of columns</label>
22 <option value="tabulation">tabulation</option>
23 <option value="semicolon">;</option>
24 <option value="comma">,</option>
25 </param>
26 <param name="dec" type="text" label="Decimal separator" value="." help="" />
27
28 <!--<param name="nr_col_names" type="integer" label="names" value="2" help="number of the column with names of metabolits" />
29 <param name="from" type="integer" label="from" value="15" help="number of the column starting peak values data (to exlude all metadata)" />
30 <param name="to" type="integer" label="to" value="30" help="number of the column finishing peak values data (to exlude all metadata)" />
31 <param name="gr_number" type="integer" label="gr_number" value="2" help="number of groups (conditions)" />
32 <param name="nb_col_gr" type="text" label="nb_col_gr" value="8,8" help="number of column of each group; separate with coma as indicated; first position coresponding to the first group etc." />
33 <param name="threshold" type="float" label="threshold" value="0.01" help="max adjusted p.value accepted" />-->
34
35 </inputs>
36
37 <outputs>
38 <data name="acp_zip" format="zip" from_work_dir="acp.zip" label="${input.name[:-4]}.pca.zip"/>
39 </outputs>
40
41 <stdio>
42 <exit_code range="1:" level="fatal" />
43 </stdio>
44
45 <help>
46
47
48 .. class:: infomark
49
50 **Authors** Gildas Le Corguille ABiMS - UPMC/CNRS - Station Biologique de Roscoff - gildas.lecorguille|at|sb-roscoff.fr
51
52 ---------------------------------------------------
53
54 ===
55 PCA
56 ===
57
58 -----------
59 Description
60 -----------
61
62
63 Performs **Principal Component Analysis (PCA)** with supplementary individuals, supplementary quantitative variables and supplementary categorical variables.
64 Missing values are replaced by the column mean. This scripts uses the FactoMineR package.
65
66
67 -----------
68 Input files
69 -----------
70
71 +---------------------------+------------+
72 | Parameter : num + label | Format |
73 +===========================+============+
74 | 1 : Data Matrix file | Tabular |
75 +---------------------------+------------+
76
77
78
79 ----------
80 Parameters
81 ----------
82
83 **Data Matrix file**
84
85 Matrix of numeric data with headers (tabular format) issued from diffreport or annotateDiffreport to make post xcms analyse .
86
87 **scale.unit**
88
89 If FALSE: no reduction of the variables
90
91 **Separator of columns:**
92
93 Type of separator for the columns
94
95 **Decimal separator:**
96
97 Type of decimal separator of the numbers in your tabular files.
98
99
100
101 ------------
102 Output files
103 ------------
104
105
106
107 **input_name.pca.zip**
108
109 | A zip file containing fours files (eigenvalue.png, percentage_of_variance.png, Rplots.pdf and Rplots1.pdf).
110
111
112 ---------------------------------------------------
113
114
115
116 ---------------
117 Working example
118 ---------------
119
120
121 Input files
122 -----------
123
124 **>A part of an example of Data Matrix file input :**
125
126
127 +--------+------------------+----------------+
128 | Name | AN7 | AN8 |
129 +========+==================+================+
130 |M102T645| 10880.0637170802 |17207.2222120537|
131 +--------+------------------+----------------+
132 |M105T604| 41911.160863452 |38105.7953589089|
133 +--------+------------------+----------------+
134
135
136
137 Parameters
138 ----------
139
140 | scale.unit -> **TRUE*
141 | Separator of columns: -> **tabulation**
142 | Decimal separator -> **.**
143
144
145
146 Output files
147 ------------
148
149
150 **eigenvalue.png:**
151
152 .. image:: pca_abims_eigenvalue.png
153
154 **percentage_of_variance.png:**
155
156 .. image:: pca_abims_percentage_of_variance.png
157
158 **Rplots.pdf:**
159
160 .. image:: pca_abims_Rplots.png
161
162 **Rplots1.pdf:**
163
164 .. image:: pca_abims_Rplots1.png
165
166
167
168
169 </help>
170
171 </tool>