Mercurial > repos > recetox > waveica
changeset 4:425c0494ec2d draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 84de3bc96ad2859d87c70ba94d8ceb0b2bc2a0da
| author | recetox |
|---|---|
| date | Tue, 07 May 2024 12:49:20 +0000 |
| parents | dbbedb14b44c |
| children | e424fa636281 |
| files | macros.xml test-data/normalized_data.csv waveica.xml waveica_wrapper.R |
| diffstat | 4 files changed, 17 insertions(+), 21 deletions(-) [+] |
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--- a/macros.xml Thu Oct 12 13:45:41 2023 +0000 +++ b/macros.xml Tue May 07 12:49:20 2024 +0000 @@ -99,7 +99,11 @@ <xml name="outputs"> <outputs> - <data format_source="data" name="normalized_data"/> + <data name="normalized_data" format="tsv"> + <change_format> + <when input_dataset="data" attribute="ext" value="parquet" format="parquet" /> + </change_format> + </data> </outputs> </xml>
--- a/test-data/normalized_data.csv Thu Oct 12 13:45:41 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -sampleName,class,sampleType,injectionOrder,batch,M85T34,M86T41,M86T518,M86T539 -VT_160120_002,sample,sample,1,1,355200.506508035,75115889.9077485,6101488.54615418,2007379.02604984 -VT_160120_004,sample,sample,2,1,216897.826587868,75204863.1495248,6170882.26270475,2069979.64992079 -VT_160120_006,sample,sample,3,1,362337.195084504,76490295.1450204,12588041.969092,1818589.63912375 -VT_160120_008,sample,sample,4,1,143303.377379009,83771659.9549148,6181538.46316058,1975712.25920485 -VT_160120_010,sample,sample,5,1,189065.516447239,84108898.7658797,6103964.42378424,1935671.32085241
--- a/waveica.xml Thu Oct 12 13:45:41 2023 +0000 +++ b/waveica.xml Tue May 07 12:49:20 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy4" python_template_version="3.5"> +<tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy5" profile="21.09"> <description>removal of batch effects for untargeted metabolomics data</description> <macros> <import>macros.xml</import> @@ -103,7 +103,7 @@ <param name="t" value="0.05"/> <param name="t2" value="0.05"/> <param name="alpha" value="0"/> - <output name="normalized_data" file="normalized_data.csv"/> + <output name="normalized_data" file="normalized_data.tsv" ftype="tsv"/> </test> <test><!-- TEST 2 --> <param name="data" value="input_data.tsv" ftype="tsv"/> @@ -114,7 +114,7 @@ <param name="t" value="0.05"/> <param name="t2" value="0.05"/> <param name="alpha" value="0"/> - <output name="normalized_data" file="normalized_data.tsv"/> + <output name="normalized_data" file="normalized_data.tsv" ftype="tsv"/> </test> <test><!-- TEST 3 --> <param name="data" value="input_data.parquet" ftype="parquet"/> @@ -125,7 +125,7 @@ <param name="t" value="0.05"/> <param name="t2" value="0.05"/> <param name="alpha" value="0"/> - <output name="normalized_data" file="normalized_data.parquet"/> + <output name="normalized_data" file="normalized_data.parquet" ftype="parquet"/> </test> <test><!-- TEST 4 --> <param name="input_choice" value="2"/> @@ -138,7 +138,7 @@ <param name="t" value="0.05"/> <param name="t2" value="0.05"/> <param name="alpha" value="0"/> - <output name="normalized_data" file="normalized_data.csv"/> + <output name="normalized_data" file="normalized_data.tsv" ftype="tsv"/> </test> <test><!-- TEST 5 --> <param name="input_choice" value="2"/> @@ -151,7 +151,7 @@ <param name="t" value="0.05"/> <param name="t2" value="0.05"/> <param name="alpha" value="0"/> - <output name="normalized_data" file="normalized_data.tsv"/> + <output name="normalized_data" file="normalized_data.tsv" ftype="tsv"/> </test> <test><!-- TEST 6 --> <param name="input_choice" value="2"/> @@ -164,7 +164,7 @@ <param name="t" value="0.05"/> <param name="t2" value="0.05"/> <param name="alpha" value="0"/> - <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200"/> + <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200" ftype="parquet"/> </test> <test><!-- TEST 7 --> <param name="input_choice" value="2"/> @@ -178,7 +178,7 @@ <param name="t" value="0.05"/> <param name="t2" value="0.05"/> <param name="alpha" value="0"/> - <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200"/> + <output name="normalized_data" file="normalized_data.parquet" compare="sim_size" delta="200" ftype="parquet"/> </test> <test><!-- TEST 8 --> <param name="input_choice" value="2"/> @@ -192,7 +192,7 @@ <param name="t" value="0.05"/> <param name="t2" value="0.05"/> <param name="alpha" value="0"/> - <output name="normalized_data" file="normalized_data.csv"/> + <output name="normalized_data" file="normalized_data.tsv" ftype="tsv"/> </test> <!-- The following test has different results on three platform I've tried --> <!-- <test>
--- a/waveica_wrapper.R Thu Oct 12 13:45:41 2023 +0000 +++ b/waveica_wrapper.R Tue May 07 12:49:20 2024 +0000 @@ -231,15 +231,13 @@ } store_data <- function(data, output, ext) { - if (ext == "csv") { - write.csv(data, file = output, row.names = FALSE, quote = FALSE) - } else if (ext == "tsv") { + if (ext == "parquet") { + arrow::write_parquet(data, output) + } else { write.table(data, file = output, sep = "\t", row.names = FALSE, quote = FALSE ) - } else { - arrow::write_parquet(data, sink = output) } cat("Normalization has been completed.\n") }