Mercurial > repos > recetox > waveica
diff waveica.xml @ 2:6480c6d5fa36 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 77bea6c84c5a932fa203723d4d5fea6147f06505
author | recetox |
---|---|
date | Fri, 23 Jun 2023 07:27:29 +0000 |
parents | b77023c41c76 |
children | dbbedb14b44c |
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--- a/waveica.xml Thu Sep 29 15:21:04 2022 +0000 +++ b/waveica.xml Fri Jun 23 07:27:29 2023 +0000 @@ -1,8 +1,9 @@ -<tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy2" python_template_version="3.5"> +<tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy3" python_template_version="3.5"> <description>removal of batch effects for untargeted metabolomics data</description> <macros> <import>macros.xml</import> </macros> + <expand macro="annotation"/> <expand macro="creator"/> <requirements> @@ -19,6 +20,7 @@ #if $input_num.input_choice == "2": metadata = "$input_num.input_metadata.metadata", ext = "$input_num.data.ext,$input_num.input_metadata.metadata.ext", + transpose = $input_num.transpose_feature_table, #else: ext = "$input_num.data.ext", #end if @@ -36,6 +38,7 @@ #if $input_num.input_choice == "2": metadata = "$input_num.input_metadata.metadata", ext = "$input_num.data.ext,$input_num.input_metadata.metadata.ext", + transpose = $input_num.transpose_feature_table, #else: ext = "$input_num.data.ext", #end if @@ -61,10 +64,12 @@ <expand macro="input_data"/> </when> <when value="2"> + <expand macro="input_data"/> <section name="input_metadata" title="Input metadata table" expanded="true"> <param name="metadata" label="Input metadata" type="data" format="csv,tsv,parquet" help="" /> - </section> - <expand macro="input_data"/> + </section> + <param name = "transpose_feature_table" label="Transpose feature table" type="boolean" checked="false" + truevalue="TRUE" falsevalue="FALSE" help="Swap sample names with feature names as column headers (to fit recetox-aplcms outputs)." /> </when> </conditional> <expand macro="general_parameters"/> @@ -93,7 +98,7 @@ <param name="data" value="input_data.csv" ftype="csv"/> <param name="mode" value="batchwise"/> <param name="wavelet_filter" value="d"/> - <param name="filter_length" value="2"/> + <param name="wavelet_length" value="2"/> <param name="k" value="20"/> <param name="t" value="0.05"/> <param name="t2" value="0.05"/> @@ -104,7 +109,7 @@ <param name="data" value="input_data.tsv" ftype="tsv"/> <param name="mode" value="batchwise"/> <param name="wavelet_filter" value="d"/> - <param name="filter_length" value="2"/> + <param name="wavelet_length" value="2"/> <param name="k" value="20"/> <param name="t" value="0.05"/> <param name="t2" value="0.05"/> @@ -115,7 +120,7 @@ <param name="data" value="input_data.parquet" ftype="parquet"/> <param name="mode" value="batchwise"/> <param name="wavelet_filter" value="d"/> - <param name="filter_length" value="2"/> + <param name="wavelet_length" value="2"/> <param name="k" value="20"/> <param name="t" value="0.05"/> <param name="t2" value="0.05"/> @@ -128,7 +133,7 @@ <param name="metadata" value="metadata.csv" ftype="csv"/> <param name="mode" value="batchwise"/> <param name="wavelet_filter" value="d"/> - <param name="filter_length" value="2"/> + <param name="wavelet_length" value="2"/> <param name="k" value="20"/> <param name="t" value="0.05"/> <param name="t2" value="0.05"/> @@ -141,7 +146,7 @@ <param name="metadata" value="metadata.tsv" ftype="tsv"/> <param name="mode" value="batchwise"/> <param name="wavelet_filter" value="d"/> - <param name="filter_length" value="2"/> + <param name="wavelet_length" value="2"/> <param name="k" value="20"/> <param name="t" value="0.05"/> <param name="t2" value="0.05"/> @@ -154,13 +159,41 @@ <param name="metadata" value="metadata.csv" ftype="csv"/> <param name="mode" value="batchwise"/> <param name="wavelet_filter" value="d"/> - <param name="filter_length" value="2"/> + <param name="wavelet_length" value="2"/> <param name="k" value="20"/> <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"/> </test> + <test><!-- TEST 7 --> + <param name="input_choice" value="2"/> + <param name="data" value="feature_table_transpose_version.parquet" ftype="parquet"/> + <param name="metadata" value="metadata.parquet" ftype="parquet"/> + <param name="transpose_feature_table" value="TRUE"/> + <param name="mode" value="batchwise"/> + <param name="wavelet_filter" value="d"/> + <param name="wavelet_length" value="2"/> + <param name="k" value="20"/> + <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"/> + </test> + <test><!-- TEST 8 --> + <param name="input_choice" value="2"/> + <param name="data" value="feature_table_transpose_version.csv" ftype="csv"/> + <param name="metadata" value="metadata.csv" ftype="csv"/> + <param name="transpose_feature_table" value="TRUE"/> + <param name="mode" value="batchwise"/> + <param name="wavelet_filter" value="d"/> + <param name="wavelet_length" value="2"/> + <param name="k" value="20"/> + <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"/> + </test> <!-- The following test has different results on three platform I've tried --> <!-- <test> <param name="data" value="input_data_nobatch.csv" ftype="csv"/>