Mercurial > repos > blankenberglab > gpca
diff r-gpca.xml @ 3:8def7dda3bee draft
planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/tools/r-gpca commit f5a03b0978b3a7473f034b87a87765ff1d65d720
| author | blankenberglab |
|---|---|
| date | Mon, 03 Dec 2018 15:04:08 -0500 |
| parents | d93629e79f5e |
| children | ceaa4d404115 |
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--- a/r-gpca.xml Tue Nov 27 12:29:58 2018 -0500 +++ b/r-gpca.xml Mon Dec 03 15:04:08 2018 -0500 @@ -56,13 +56,16 @@ <output name="html_outfile" ftype="html" file="html_outfile_1/html_outfile_1.html"> <extra_files type="file" name="gDist_1.png" value="html_outfile_1/gDist_1.png" compare="sim_size"/> <extra_files type="file" name="guided_1v2_1.png" value="html_outfile_1/guided_1v2_1.png" compare="sim_size"/> - <extra_files type="file" name="unguided_1v2_1.png" value="html_outfile_1/unguided_1v2_1.png" compare="sim_size"/> + <extra_files type="file" name="unguided_1v2_1.png" value="html_outfile_1/unguided_1v2_1.png" + compare="sim_size"/> <extra_files type="file" name="guided_npcs_1.png" value="html_outfile_1/guided_npcs_1.png" compare="sim_size"/> - <extra_files type="file" name="unguided_npcs_1.png" value="html_outfile_1/unguided_npcs_1.png" compare="sim_size"/> + <extra_files type="file" name="unguided_npcs_1.png" value="html_outfile_1/unguided_npcs_1.png" + compare="sim_size"/> <extra_files type="file" name="guided_var_1.png" value="html_outfile_1/guided_var_1.png" compare="sim_size"/> - <extra_files type="file" name="unguided_var_1.png" value="html_outfile_1/unguided_var_1.png" compare="sim_size"/> + <extra_files type="file" name="unguided_var_1.png" value="html_outfile_1/unguided_var_1.png" + compare="sim_size"/> </output> - <output name="numbers_outfile" ftype="tabular" file="numbers_outfile_1.tabular"/> + <output name="numbers_outfile_1.tabular" ftype="tabular" file="numbers_outfile_1.tabular"/> </test> <test> <param name="batch" ftype="tabular" value="batch_in_multiple_1.tabular" /> @@ -78,18 +81,22 @@ <extra_files type="file" name="gDist_2.png" value="html_outfile_2/gDist_2.png" compare="sim_size"/> <extra_files type="file" name="guided_1v2_1.png" value="html_outfile_2/guided_1v2_1.png" compare="sim_size"/> <extra_files type="file" name="guided_1v2_2.png" value="html_outfile_2/guided_1v2_2.png" compare="sim_size"/> - <extra_files type="file" name="unguided_1v2_1.png" value="html_outfile_2/unguided_1v2_1.png" compare="sim_size"/> - <extra_files type="file" name="unguided_1v2_2.png" value="html_outfile_2/unguided_1v2_2.png" compare="sim_size"/> + <extra_files type="file" name="unguided_1v2_1.png" value="html_outfile_2/unguided_1v2_1.png" + compare="sim_size"/> + <extra_files type="file" name="unguided_1v2_2.png" value="html_outfile_2/unguided_1v2_2.png" + compare="sim_size"/> <extra_files type="file" name="guided_npcs_1.png" value="html_outfile_2/guided_npcs_1.png" compare="sim_size"/> <extra_files type="file" name="guided_npcs_2.png" value="html_outfile_2/guided_npcs_2.png" compare="sim_size"/> <extra_files type="file" name="unguided_npcs_1.png" value="html_outfile_2/unguided_npcs_1.png" compare="sim_size"/> <extra_files type="file" name="unguided_npcs_2.png" value="html_outfile_2/unguided_npcs_2.png" compare="sim_size"/> <extra_files type="file" name="guided_var_1.png" value="html_outfile_2/guided_var_1.png" compare="sim_size"/> <extra_files type="file" name="guided_var_2.png" value="html_outfile_2/guided_var_2.png" compare="sim_size"/> - <extra_files type="file" name="unguided_var_1.png" value="html_outfile_2/unguided_var_1.png" compare="sim_size"/> - <extra_files type="file" name="unguided_var_2.png" value="html_outfile_2/unguided_var_2.png" compare="sim_size"/> + <extra_files type="file" name="unguided_var_1.png" value="html_outfile_2/unguided_var_1.png" + compare="sim_size"/> + <extra_files type="file" name="unguided_var_2.png" value="html_outfile_2/unguided_var_2.png" + compare="sim_size"/> </output> - <output name="numbers_outfile" ftype="tabular" file="numbers_outfile_2.tabular"/> + <output name="numbers_outfile_2.tabular" ftype="tabular" file="numbers_outfile_2.tabular"/> </test> </tests> @@ -118,13 +125,11 @@ npcs: number of principal components to calculate **Literature** - https://cran.r-project.org/web/packages/gPCA/gPCA.pdf https://cran.r-project.org/web/packages/gPCA/vignettes/gPCA.pdf **Input File Help** - Batch: The batch file must be a tab delimited file. It will be read as a numeric vector, consisting of as many different batches as you like. The test data file batch_in_multiple_1.tabular shows the correct format. The length of batch must conform to the data matrix or an error will occur. Data: The data file must be a tab delimited file. It will be read in as a matrix. The test data file data_in_1.tabular shows the correct format. If you are receving errors about nonconformed matrices in your matrix you might need to transpose your matrix before using it in the tool.