Mercurial > repos > bgruening > deeptools_plot_pca
comparison plotPCA.xml @ 12:814bea57a4fe draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
author | bgruening |
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date | Fri, 31 Mar 2017 09:28:03 -0400 |
parents | 18fad2642adc |
children | dfe535b75616 |
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11:fc06f0b21c23 | 12:814bea57a4fe |
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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" /> |