annotate PCA_plot.xml @ 9:2e8c9032e8d8 draft

Uploaded
author mb2013
date Tue, 20 May 2014 03:27:01 -0400
parents 0cb68fb9010f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
1 <tool id="PCA_plot" name="PCA_plot">
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
2 <description>Plottool for Principal Component </description>
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
3 <command interpreter="Rscript">PCA_plot.R $input "$title" "$x_label" "$y_label" $x_column $y_column $names $output</command>
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
4 <inputs>
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
5 <param name="input" type="data" format="csv" label="PCA coordinates" />
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
6 <param name = "title" size = "30" type = "text" value = "" label = "Main Title"/>
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
7 <param name = "x_label" size = "30" type = "text" value = "" label = "x axis label"/>
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
8 <param name = "y_label" size = "30" type = "text" value = "" label = "y axis label"/>
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
9 <param name = "x_column" size = "2" type = "integer" value = "1" label = "pca x axis"/>
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
10 <param name = "y_column" size = "2" type = "integer" value = "2" label = "pca y axis"/>
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
11 <param name = "names" type = "data" format = "csv" label = "data names"/>
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
12 </inputs>
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
13 <outputs>
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
14 <data format="png" name="output" />
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
15 </outputs>
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
16
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
17
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
18 <help>
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
19 **Function**
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
20
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
21 Plottool for plotting of Principal Components
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
22
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
23 **Input file**
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
24
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
25 Principal Components coordinates (csv format)
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
26
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
27 sample names (csv format)
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
28
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
29 **Tip**
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
30
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
31 Use **PCA** to generate Principal Components
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
32
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
33 Use the sample names of **DtaConverter** or create your own 'sample name file' in .csv format
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
34 </help>
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
35
0cb68fb9010f Uploaded
mb2013
parents:
diff changeset
36 </tool>