Mercurial > repos > recetox > recetox_aplcms_unsupervised
diff recetox_aplcms_unsupervised.xml @ 11:e0f77e03599e draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
| author | recetox |
|---|---|
| date | Fri, 28 Jan 2022 16:26:05 +0000 |
| parents | 6057540f65a9 |
| children | 6eeeebc35909 |
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--- a/recetox_aplcms_unsupervised.xml Thu Oct 21 15:03:18 2021 +0000 +++ b/recetox_aplcms_unsupervised.xml Fri Jan 28 16:26:05 2022 +0000 @@ -1,14 +1,15 @@ <tool id="recetox_aplcms_unsupervised" name="RECETOX apLCMS Unsupervised" version="@TOOL_VERSION@+galaxy2"> <description>generate a feature table from LC/MS spectra</description> <macros> - <import>recetox_aplcms_macros.xml</import> + <import>macros.xml</import> </macros> - <expand macro="requirements" /> + <expand macro="creator"/> + + <expand macro="requirements"/> <command detect_errors="aggressive"><![CDATA[ sh ${symlink_inputs} && Rscript -e 'source("${__tool_directory__}/main.R")' -e 'source("${run_script}")' ]]></command> - <expand macro="creator" /> <configfiles> <configfile name="symlink_inputs"> #for $infile in $files @@ -52,37 +53,37 @@ </configfiles> <expand macro="inputs"> - <expand macro="noise_filtering" /> - <expand macro="feature_detection" /> - <expand macro="peak_alignment" /> - <expand macro="weak_signal_recovery" /> - <expand macro="output_format" /> + <expand macro="noise_filtering"/> + <expand macro="feature_detection"/> + <expand macro="peak_alignment"/> + <expand macro="weak_signal_recovery"/> + <expand macro="output_format"/> </expand> <outputs> - <expand macro="unsupervised_outputs" /> + <expand macro="unsupervised_outputs"/> </outputs> <tests> <test> - <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml" /> - <output name="recovered_feature_sample_table" file="unsupervised_recovered_feature_sample_table.parquet" ftype="parquet"/> + <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/> + <output name="recovered_feature_sample_table" file="unsupervised_recovered_feature_sample_table.parquet" + ftype="parquet"/> </test> <test> - <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml" /> + <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/> <section name="output_format"> - <param name="out_format" value="recetox" /> + <param name="out_format" value="recetox"/> </section> <output name="recovered_feature_sample_table" file="unsupervised.recetox.parquet" ftype="parquet"/> </test> </tests> <help> - This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or - any historically detected features. For such functionality please use the Hybrid version of apLCMS. - - @GENERAL_HELP@ + <![CDATA[ + @HELP_unsupervised@ + ]]> </help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>