Mercurial > repos > bgruening > deeptools_plot_pca

comparison plotPCA.xml @ 12:814bea57a4fe 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 09975f870c75347fba5c6777c9f3b442bdeeb289
author bgruening
date Fri, 31 Mar 2017 09:28:03 -0400
parents 18fad2642adc
children dfe535b75616
comparison
equal deleted inserted replaced
11:fc06f0b21c23 12:814bea57a4fe
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 $rowCenter
15 #if $outFileNameData 16 #if $outFileNameData
16 --outFileNameData "$output_outFileNameData" 17 --outFileNameData "$output_outFileNameData"
17 #end if 18 #end if
18 ]]> 19 ]]>
19 </command> 20 </command>
20 <inputs> 21 <inputs>
21 <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the multiBamSummary or multiBigwigSummary tools"/> 22 <param name="corData" format="deeptools_coverage_matrix" type="data" label="Matrix file from the multiBamSummary or multiBigwigSummary tools"/>
22 <expand macro="input_image_file_format" /> 23 <expand macro="input_image_file_format" />
23 <expand macro="plotTitle" /> 24 <expand macro="plotTitle" />
24 <param argument="--outFileNameData" type="boolean" label="Save the matrix of PCA and eigenvalues underlying the plot."/> 25 <param argument="--outFileNameData" type="boolean" label="Save the matrix of PCA and eigenvalues underlying the plot."/>
26 <param argument="--rowCenter" type="boolean" label="Center Rows?" help="When specified, each row (bin, gene, etc.) in the matrix is centered at 0 before the PCA is computed. This is useful only if you have a strong bin/gene/etc. correlation and the resulting principal component has samples stacked vertically." truevalue="--rowCenter" falsevalue="" />
25 </inputs> 27 </inputs>
26 <outputs> 28 <outputs>
27 <expand macro="output_image_file_format_not_nested" /> 29 <expand macro="output_image_file_format_not_nested" />
28 <data format="tabular" name="output_outFileNameData" label="${tool.name} on ${on_string}: PCA matrix"> 30 <data format="tabular" name="output_outFileNameData" label="${tool.name} on ${on_string}: PCA matrix">
29 <filter>outFileNameData</filter> 31 <filter>outFileNameData</filter>
30 </data> 32 </data>
31 </outputs> 33 </outputs>
32 <tests> 34 <tests>
33 <test> 35 <test>
34 <param name="corData" value="multiBamSummary_result2.npz" ftype="deeptools_coverage_matrix" /> 36 <param name="corData" value="multiBamSummary_result2b.npz" ftype="deeptools_coverage_matrix" />
35 <param name="plotTitle" value="Test Plot" /> 37 <param name="plotTitle" value="Test Plot" />
36 <param name="outFileFormat" value="png" /> 38 <param name="outFileFormat" value="png" />
37 <output name="outFileName" file="plotPCA_result1.png" ftype="png" compare="sim_size" delta="4000" /> 39 <output name="outFileName" file="plotPCA_result1.png" ftype="png" compare="sim_size" delta="4000" />
38 </test> 40 </test>
39 <test> 41 <test>
40 <param name="corData" value="multiBamSummary_result2.npz" ftype="deeptools_coverage_matrix" /> 42 <param name="corData" value="multiBamSummary_result2b.npz" ftype="deeptools_coverage_matrix" />
41 <param name="plotTitle" value="Test Plot" /> 43 <param name="plotTitle" value="Test Plot" />
42 <param name="outFileFormat" value="png" /> 44 <param name="outFileFormat" value="png" />
43 <param name="outFileNameData" value="True" /> 45 <param name="outFileNameData" value="True" />
44 <output name="outFileName" file="plotPCA_result2.png" ftype="png" compare="sim_size" delta="4000" /> 46 <output name="outFileName" file="plotPCA_result2.png" ftype="png" compare="sim_size" delta="4000" />
45 <output name="output_outFileNameData" file="plotPCA_result2.tabular" ftype="tabular" /> 47 <output name="output_outFileNameData" file="plotPCA_result2.tabular" ftype="tabular" />