Mercurial > repos > bgruening > deeptools_plot_pca

comparison plotPCA.xml @ 28:beb7f689a761 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
author bgruening
date Sun, 14 May 2017 18:54:46 -0400
parents 5150510cd7e4
children 94d2a13a344d
comparison
equal deleted inserted replaced
27:5150510cd7e4 28:beb7f689a761
10 @BINARY@ 10 @BINARY@
11 --corData "$corData" 11 --corData "$corData"
12 --plotTitle "$plotTitle" 12 --plotTitle "$plotTitle"
13 --plotFile "$outFileName" 13 --plotFile "$outFileName"
14 --plotFileFormat "$outFileFormat" 14 --plotFileFormat "$outFileFormat"
15 #if str($advancedOpt.showAdvancedOpt) == 'yes':
16 @PLOTWIDTHHEIGHT@
17 #end if
15 $rowCenter 18 $rowCenter
16 #if $outFileNameData 19 #if $outFileNameData
17 --outFileNameData "$output_outFileNameData" 20 --outFileNameData "$output_outFileNameData"
18 #end if 21 #end if
19 ]]> 22 ]]>
22 <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the multiBamSummary or multiBigwigSummary tools"/> 25 <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the multiBamSummary or multiBigwigSummary tools"/>
23 <expand macro="input_image_file_format" /> 26 <expand macro="input_image_file_format" />
24 <expand macro="plotTitle" /> 27 <expand macro="plotTitle" />
25 <param argument="--outFileNameData" type="boolean" label="Save the matrix of PCA and eigenvalues underlying the plot."/> 28 <param argument="--outFileNameData" type="boolean" label="Save the matrix of PCA and eigenvalues underlying the plot."/>
26 <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." truevalue="--rowCenter" falsevalue="" /> 29 <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." truevalue="--rowCenter" falsevalue="" />
30 <conditional name="advancedOpt">
31 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
32 <option value="no" selected="true">no</option>
33 <option value="yes">yes</option>
34 </param>
35 <when value="no" />
36 <when value="yes">
37 <expand macro="plotWidthHeight" PLOTWIDTH="5.0" PLOTHEIGHT="10.0" />
38 </when>
39 </conditional>
27 </inputs> 40 </inputs>
28 <outputs> 41 <outputs>
29 <expand macro="output_image_file_format_not_nested" /> 42 <expand macro="output_image_file_format_not_nested" />
30 <data format="tabular" name="output_outFileNameData" label="${tool.name} on ${on_string}: PCA matrix"> 43 <data format="tabular" name="output_outFileNameData" label="${tool.name} on ${on_string}: PCA matrix">
31 <filter>outFileNameData</filter> 44 <filter>outFileNameData</filter>