Mercurial > repos > recetox > recetox_aplcms_recover_weaker_signals
changeset 1:f9fb9d8fb710 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 699355cdf45b2157e9eea3962a01950d469fb0ba
| author | recetox |
|---|---|
| date | Thu, 16 Jun 2022 10:27:28 +0000 |
| parents | 067a308223e3 |
| children | 472dc85ce7c5 |
| files | recetox_aplcms_recover_weaker_signals.xml |
| diffstat | 1 files changed, 30 insertions(+), 14 deletions(-) [+] |
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--- a/recetox_aplcms_recover_weaker_signals.xml Fri Jun 10 10:18:24 2022 +0000 +++ b/recetox_aplcms_recover_weaker_signals.xml Thu Jun 16 10:27:28 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="recetox_aplcms_recover_weaker_signals" name="RECETOX apLCMS - recover weaker signals" version="@TOOL_VERSION@+galaxy0"> +<tool id="recetox_aplcms_recover_weaker_signals" name="RECETOX apLCMS - recover weaker signals" version="@TOOL_VERSION@+galaxy1"> <description>recover weaker signals from LC/MS spectra</description> <macros> <import>macros.xml</import> @@ -17,7 +17,7 @@ ln -s '${infile}' '${infile.element_identifier}' #end for #for $infile in $extracted_files - ln -s '${infile}' '${infile.element_identifier}' + ln -s '${infile}' 'extracted_${infile.element_identifier}' #end for #for $infile in $corrected_files ln -s '${infile}' '${infile.element_identifier}' @@ -27,7 +27,7 @@ #set filenames = str("', '").join([str($f.element_identifier) for $f in $ms_files]) filenames <- sort_samples_by_acquisition_number(c('$filenames')) - #set extracted_files = str("', '").join([str($f.element_identifier) for $f in $extracted_files]) + #set extracted_files = str("', '").join(["extracted_" + str($f.element_identifier) for $f in $extracted_files]) extracted <- load_features(c('$extracted_files')) #set corrected_files = str("', '").join([str($f.element_identifier) for $f in $corrected_files]) @@ -62,12 +62,12 @@ </configfiles> <inputs> - <param name="ms_files" type="data" format="mzdata,mzml,mzxml,netcdf" multiple="true" min="2" label="Input data" - help="Mass spectrometry file for peak extraction." /> - <param name="extracted_files" type="data" format="parquet" multiple="true" min="2" label="Input extracted feature samples" - help="Mass spectrometry files containing feature samples." /> - <param name="corrected_files" type="data" format="parquet" multiple="true" min="2" label="Input corrected feature samples" - help="Mass spectrometry file containing corrected feature samples." /> + <param name="ms_files" type="data_collection" collection_type="list" format="mzdata,mzml,mzxml,netcdf" + label="Input data collection" help="Mass spectrometry file for peak extraction." /> + <param name="extracted_files" type="data_collection" collection_type="list" format="parquet" + label="Input extracted feature samples collection" help="Mass spectrometry files containing feature samples." /> + <param name="corrected_files" type="data_collection" collection_type="list" format="parquet" + label="Input corrected feature samples collection" help="Mass spectrometry file containing corrected feature samples." /> <param name="tolerances_file" type="data" format="parquet" label="Input tolerances" help="TBD"/> <param name="rt_cross_table_file" type="data" format="parquet" label="Input rt cross table" help="TBD"/> <param name="int_cross_table_file" type="data" format="parquet" label="Input int cross table" help="TBD"/> @@ -93,11 +93,27 @@ <tests> <test> - <param name="ms_files" value="mbr_test2.mzml,mbr_test1.mzml,mbr_test0.mzml" ftype="mzml"/> - <param name="extracted_files" ftype="parquet" - value="extracted_expected/extracted_0.parquet,extracted_expected/extracted_1.parquet,extracted_expected/extracted_2.parquet"/> - <param name="corrected_files" ftype="parquet" - value="corrected_expected/corrected_0.parquet,corrected_expected/corrected_1.parquet,corrected_expected/corrected_2.parquet"/> + <param name="ms_files"> + <collection type="list"> + <element name="mbr_test0.mzml" value="mbr_test0.mzml"/> + <element name="mbr_test1.mzml" value="mbr_test1.mzml"/> + <element name="mbr_test2.mzml" value="mbr_test2.mzml"/> + </collection> + </param> + <param name="extracted_files"> + <collection type="list"> + <element name="extracted_features_0.parquet" value="extracted_expected/extracted_0.parquet"/> + <element name="extracted_features_1.parquet" value="extracted_expected/extracted_1.parquet"/> + <element name="extracted_features_2.parquet" value="extracted_expected/extracted_2.parquet"/> + </collection> + </param> + <param name="corrected_files"> + <collection type="list"> + <element name="corrected_features_0.parquet" value="corrected_expected/corrected_0.parquet"/> + <element name="corrected_features_1.parquet" value="corrected_expected/corrected_1.parquet"/> + <element name="corrected_features_2.parquet" value="corrected_expected/corrected_2.parquet"/> + </collection> + </param> <param name="tolerances_file" value="tolerances.parquet" ftype="parquet"/> <param name="rt_cross_table_file" value="rt_cross_table.parquet" ftype="parquet"/> <param name="int_cross_table_file" value="int_cross_table.parquet" ftype="parquet"/>