Mercurial > repos > bgruening > deeptools_plot_pca

annotate plotPCA.xml @ 32:94d2a13a344d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
author bgruening
date Thu, 15 Feb 2018 04:13:20 -0500
parents beb7f689a761
children 528355f62f3a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
27
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
1 <tool id="deeptools_plot_pca" name="plotPCA" version="@WRAPPER_VERSION@.0">
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
2 <description>Generate principal component analysis (PCA) plots from multiBamSummary or multiBigwigSummary output</description>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
3 <macros>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
4 <token name="@BINARY@">plotPCA</token>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
5 <import>deepTools_macros.xml</import>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
6 </macros>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
7 <expand macro="requirements"/>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
8 <command>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
9 <![CDATA[
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
10 @BINARY@
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
11 --corData "$corData"
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
12 --plotTitle "$plotTitle"
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
13 --plotFile "$outFileName"
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
14 --plotFileFormat "$outFileFormat"
28
beb7f689a761 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
bgruening
parents: 27
diff changeset
15 #if str($advancedOpt.showAdvancedOpt) == 'yes':
beb7f689a761 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
bgruening
parents: 27
diff changeset
16 @PLOTWIDTHHEIGHT@
32
94d2a13a344d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 28
diff changeset
17 $advancedOpt.log2
94d2a13a344d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 28
diff changeset
18 --PCs $advancedOpt.PCs
94d2a13a344d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 28
diff changeset
19 --ntop $advancedOpt.ntop
94d2a13a344d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 28
diff changeset
20 $advancedOpt.transpose
94d2a13a344d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 28
diff changeset
21 $advancedOpt.rowCenter
94d2a13a344d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 28
diff changeset
22 #if $advancedOpt.colors:
94d2a13a344d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 28
diff changeset
23 --colors $advancedOpt.colors
94d2a13a344d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 28
diff changeset
24 #end if
28
beb7f689a761 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
bgruening
parents: 27
diff changeset
25 #end if
27
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
26 #if $outFileNameData
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
27 --outFileNameData "$output_outFileNameData"
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
28 #end if
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
29 ]]>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
30 </command>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
31 <inputs>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
32 <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the multiBamSummary or multiBigwigSummary tools"/>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
33 <expand macro="input_image_file_format" />
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
34 <expand macro="plotTitle" />
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
35 <param argument="--outFileNameData" type="boolean" label="Save the matrix of PCA and eigenvalues underlying the plot."/>
28
beb7f689a761 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
bgruening
parents: 27
diff changeset
36 <conditional name="advancedOpt">
beb7f689a761 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
bgruening
parents: 27
diff changeset
37 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
beb7f689a761 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
bgruening
parents: 27
diff changeset
38 <option value="no" selected="true">no</option>
beb7f689a761 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
bgruening
parents: 27
diff changeset
39 <option value="yes">yes</option>
beb7f689a761 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
bgruening
parents: 27
diff changeset
40 </param>
beb7f689a761 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
bgruening
parents: 27
diff changeset
41 <when value="no" />
beb7f689a761 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
bgruening
parents: 27
diff changeset
42 <when value="yes">
beb7f689a761 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
bgruening
parents: 27
diff changeset
43 <expand macro="plotWidthHeight" PLOTWIDTH="5.0" PLOTHEIGHT="10.0" />
32
94d2a13a344d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 28
diff changeset
44 <param name="PCs" argument="--PCs" label="Principal components to plot" value="1 2" type="text"
94d2a13a344d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 28
diff changeset
45 help="The principal components to plot. If specified, you must provide two different integers, greater than zero, separated by a space. An example (and the default) is '1 2'." />
94d2a13a344d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 28
diff changeset
46 <param name="ntop" argument="--ntop" label="Number of rows to use" value="1000" type="integer"
94d2a13a344d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 28
diff changeset
47 help="Use only the top N most variable rows in the original matrix. Specifying 0 will result in all rows being used. If the matrix is to be transposed, rows with 0 variance are always excluded, even if a values of 0 is specified. The default is 1000." />
94d2a13a344d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 28
diff changeset
48 <param name="log2" argument="--log2" type="boolean" truevalue="--log2" falsevalue="" label="log2 transform data" help="log2 transform the datapoints prior to computing the PCA. Note that 0.01 is added to all values to prevent 0 values from becoming -infinity. Using this option with input that contains negative values will result in an error." />
94d2a13a344d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 28
diff changeset
49 <param argument="--transpose" type="boolean" label="Transpose Matrix?" help="Perform the PCA on the transpose of the matrix, (i.e., with samples as rows and features/genes as columns). This then matches what is typically done in R for RNAseq data." truevalue="--transpose" falsevalue="" />
94d2a13a344d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 28
diff changeset
50 <param argument="--rowCenter" type="boolean" label="Center Rows?" help="When specified, each row (bin, gene, etc.) in the matrix is centered at 0 before the PCA is computed. This is useful only if you have a strong bin/gene/etc. correlation and the resulting principal component has samples stacked vertically. This option is not applicable if the PCA is performed on the transposed matrix." truevalue="--rowCenter" falsevalue="" />
94d2a13a344d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 28
diff changeset
51 <param argument="--colors" type="text" name="colors" label="Symbol colors" value="" optional="True"
94d2a13a344d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 28
diff changeset
52 help="A list of colors for the symbols. Color names and html hex string (e.g., #eeff22) are accepted. The color names should be space separated. For example, --colors 'red blue green'. If not specified, the symbols will be given automatic colors." />
28
beb7f689a761 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
bgruening
parents: 27
diff changeset
53 </when>
beb7f689a761 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
bgruening
parents: 27
diff changeset
54 </conditional>
27
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
55 </inputs>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
56 <outputs>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
57 <expand macro="output_image_file_format_not_nested" />
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
58 <data format="tabular" name="output_outFileNameData" label="${tool.name} on ${on_string}: PCA matrix">
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
59 <filter>outFileNameData</filter>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
60 </data>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
61 </outputs>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
62 <tests>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
63 <test>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
64 <param name="corData" value="multiBamSummary_result2b.npz" ftype="deeptools_coverage_matrix" />
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
65 <param name="plotTitle" value="Test Plot" />
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
66 <param name="outFileFormat" value="png" />
32
94d2a13a344d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 28
diff changeset
67 <param name="showAdvancedOpt" value="yes" />
94d2a13a344d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 28
diff changeset
68 <output name="outFileName" file="plotPCA_result1.png" ftype="png" compare="sim_size" delta="12000" />
27
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
69 </test>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
70 <test>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
71 <param name="corData" value="multiBamSummary_result2b.npz" ftype="deeptools_coverage_matrix" />
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
72 <param name="plotTitle" value="Test Plot" />
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
73 <param name="outFileFormat" value="png" />
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
74 <param name="outFileNameData" value="True" />
32
94d2a13a344d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 28
diff changeset
75 <output name="outFileName" file="plotPCA_result2.png" ftype="png" compare="sim_size" delta="12000" />
27
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
76 <output name="output_outFileNameData" file="plotPCA_result2.tabular" ftype="tabular" />
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
77 </test>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
78 </tests>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
79 <help>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
80 <![CDATA[
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
81
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
82 What it does
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
83 ------------
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
84
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
85 This tool takes the **default output file** of ``multiBamSummary`` or ``multiBigwigSummary`` to perform a principal component analysis (PCA).
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
86
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
87 Output
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
88 ------
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
89
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
90 The result is a panel of two plots:
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
91
32
94d2a13a344d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 28
diff changeset
92 1. Either the loadings (default) or the projections (``--transpose``) of the samples on the desired **two principal components**.
94d2a13a344d planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty
bgruening
parents: 28
diff changeset
93 2. The **Scree plot** for principal components where the bars represent the eigenvalues the red line traces the amount of variability is explained by the individual components in a cumulative manner.
27
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
94
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
95 Example plot
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
96 ------------
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
97
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
98 .. image:: $PATH_TO_IMAGES/plotPCA_annotated.png
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
99 :width: 600
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
100 :height: 315
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
101
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
102 -----
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
103
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
104 Theoretical Background
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
105 ----------------------
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
106
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
107 Principal component analysis (PCA) can be used, for example, to determine whether **samples display greater variability** between experimental conditions than between replicates of the same treatment. PCA is also useful to identify unexpected patterns, such as those caused by batch effects or outliers.
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
108 Principal components represent the directions along which the variation in the data is maximal, so that the information (e.g., read coverage values) from thousands of regions can be represented by just a few dimensions.
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
109
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
110 PCA is not necessarily meant to identify unknown groupings or clustering; it is up to the researcher to determine the experimental or technical reason underlying the principal components.
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
111
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
112
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
113 -----
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
114
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
115 @REFERENCES@
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
116 ]]>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
117 </help>
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
118 <expand macro="citations" />
5150510cd7e4 planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit bb937143059a50d8181d7c43a0bf7284f991a5ae
bgruening
parents: 24
diff changeset
119 </tool>