Mercurial > repos > recetox > recetox_aplcms_recover_weaker_signals
comparison recetox_aplcms_recover_weaker_signals.xml @ 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 |
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| 0:067a308223e3 | 1:f9fb9d8fb710 |
|---|---|
| 1 <tool id="recetox_aplcms_recover_weaker_signals" name="RECETOX apLCMS - recover weaker signals" version="@TOOL_VERSION@+galaxy0"> | 1 <tool id="recetox_aplcms_recover_weaker_signals" name="RECETOX apLCMS - recover weaker signals" version="@TOOL_VERSION@+galaxy1"> |
| 2 <description>recover weaker signals from LC/MS spectra</description> | 2 <description>recover weaker signals from LC/MS spectra</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 <import>macros_split.xml</import> | 5 <import>macros_split.xml</import> |
| 6 </macros> | 6 </macros> |
| 15 <configfile name="symlink_inputs"> | 15 <configfile name="symlink_inputs"> |
| 16 #for $infile in $ms_files | 16 #for $infile in $ms_files |
| 17 ln -s '${infile}' '${infile.element_identifier}' | 17 ln -s '${infile}' '${infile.element_identifier}' |
| 18 #end for | 18 #end for |
| 19 #for $infile in $extracted_files | 19 #for $infile in $extracted_files |
| 20 ln -s '${infile}' '${infile.element_identifier}' | 20 ln -s '${infile}' 'extracted_${infile.element_identifier}' |
| 21 #end for | 21 #end for |
| 22 #for $infile in $corrected_files | 22 #for $infile in $corrected_files |
| 23 ln -s '${infile}' '${infile.element_identifier}' | 23 ln -s '${infile}' '${infile.element_identifier}' |
| 24 #end for | 24 #end for |
| 25 </configfile> | 25 </configfile> |
| 26 <configfile name="run_script"><![CDATA[ | 26 <configfile name="run_script"><![CDATA[ |
| 27 #set filenames = str("', '").join([str($f.element_identifier) for $f in $ms_files]) | 27 #set filenames = str("', '").join([str($f.element_identifier) for $f in $ms_files]) |
| 28 filenames <- sort_samples_by_acquisition_number(c('$filenames')) | 28 filenames <- sort_samples_by_acquisition_number(c('$filenames')) |
| 29 | 29 |
| 30 #set extracted_files = str("', '").join([str($f.element_identifier) for $f in $extracted_files]) | 30 #set extracted_files = str("', '").join(["extracted_" + str($f.element_identifier) for $f in $extracted_files]) |
| 31 extracted <- load_features(c('$extracted_files')) | 31 extracted <- load_features(c('$extracted_files')) |
| 32 | 32 |
| 33 #set corrected_files = str("', '").join([str($f.element_identifier) for $f in $corrected_files]) | 33 #set corrected_files = str("', '").join([str($f.element_identifier) for $f in $corrected_files]) |
| 34 corrected <- load_features(c('$corrected_files')) | 34 corrected <- load_features(c('$corrected_files')) |
| 35 | 35 |
| 60 '$output_format.out_format') | 60 '$output_format.out_format') |
| 61 ]]></configfile> | 61 ]]></configfile> |
| 62 </configfiles> | 62 </configfiles> |
| 63 | 63 |
| 64 <inputs> | 64 <inputs> |
| 65 <param name="ms_files" type="data" format="mzdata,mzml,mzxml,netcdf" multiple="true" min="2" label="Input data" | 65 <param name="ms_files" type="data_collection" collection_type="list" format="mzdata,mzml,mzxml,netcdf" |
| 66 help="Mass spectrometry file for peak extraction." /> | 66 label="Input data collection" help="Mass spectrometry file for peak extraction." /> |
| 67 <param name="extracted_files" type="data" format="parquet" multiple="true" min="2" label="Input extracted feature samples" | 67 <param name="extracted_files" type="data_collection" collection_type="list" format="parquet" |
| 68 help="Mass spectrometry files containing feature samples." /> | 68 label="Input extracted feature samples collection" help="Mass spectrometry files containing feature samples." /> |
| 69 <param name="corrected_files" type="data" format="parquet" multiple="true" min="2" label="Input corrected feature samples" | 69 <param name="corrected_files" type="data_collection" collection_type="list" format="parquet" |
| 70 help="Mass spectrometry file containing corrected feature samples." /> | 70 label="Input corrected feature samples collection" help="Mass spectrometry file containing corrected feature samples." /> |
| 71 <param name="tolerances_file" type="data" format="parquet" label="Input tolerances" help="TBD"/> | 71 <param name="tolerances_file" type="data" format="parquet" label="Input tolerances" help="TBD"/> |
| 72 <param name="rt_cross_table_file" type="data" format="parquet" label="Input rt cross table" help="TBD"/> | 72 <param name="rt_cross_table_file" type="data" format="parquet" label="Input rt cross table" help="TBD"/> |
| 73 <param name="int_cross_table_file" type="data" format="parquet" label="Input int cross table" help="TBD"/> | 73 <param name="int_cross_table_file" type="data" format="parquet" label="Input int cross table" help="TBD"/> |
| 74 <expand macro="mz_tol_macro"/> | 74 <expand macro="mz_tol_macro"/> |
| 75 <param name="min_bandwidth" type="float" optional="true" label="min_bandwidth (optional)" | 75 <param name="min_bandwidth" type="float" optional="true" label="min_bandwidth (optional)" |
| 91 </expand> | 91 </expand> |
| 92 </outputs> | 92 </outputs> |
| 93 | 93 |
| 94 <tests> | 94 <tests> |
| 95 <test> | 95 <test> |
| 96 <param name="ms_files" value="mbr_test2.mzml,mbr_test1.mzml,mbr_test0.mzml" ftype="mzml"/> | 96 <param name="ms_files"> |
| 97 <param name="extracted_files" ftype="parquet" | 97 <collection type="list"> |
| 98 value="extracted_expected/extracted_0.parquet,extracted_expected/extracted_1.parquet,extracted_expected/extracted_2.parquet"/> | 98 <element name="mbr_test0.mzml" value="mbr_test0.mzml"/> |
| 99 <param name="corrected_files" ftype="parquet" | 99 <element name="mbr_test1.mzml" value="mbr_test1.mzml"/> |
| 100 value="corrected_expected/corrected_0.parquet,corrected_expected/corrected_1.parquet,corrected_expected/corrected_2.parquet"/> | 100 <element name="mbr_test2.mzml" value="mbr_test2.mzml"/> |
| 101 </collection> | |
| 102 </param> | |
| 103 <param name="extracted_files"> | |
| 104 <collection type="list"> | |
| 105 <element name="extracted_features_0.parquet" value="extracted_expected/extracted_0.parquet"/> | |
| 106 <element name="extracted_features_1.parquet" value="extracted_expected/extracted_1.parquet"/> | |
| 107 <element name="extracted_features_2.parquet" value="extracted_expected/extracted_2.parquet"/> | |
| 108 </collection> | |
| 109 </param> | |
| 110 <param name="corrected_files"> | |
| 111 <collection type="list"> | |
| 112 <element name="corrected_features_0.parquet" value="corrected_expected/corrected_0.parquet"/> | |
| 113 <element name="corrected_features_1.parquet" value="corrected_expected/corrected_1.parquet"/> | |
| 114 <element name="corrected_features_2.parquet" value="corrected_expected/corrected_2.parquet"/> | |
| 115 </collection> | |
| 116 </param> | |
| 101 <param name="tolerances_file" value="tolerances.parquet" ftype="parquet"/> | 117 <param name="tolerances_file" value="tolerances.parquet" ftype="parquet"/> |
| 102 <param name="rt_cross_table_file" value="rt_cross_table.parquet" ftype="parquet"/> | 118 <param name="rt_cross_table_file" value="rt_cross_table.parquet" ftype="parquet"/> |
| 103 <param name="int_cross_table_file" value="int_cross_table.parquet" ftype="parquet"/> | 119 <param name="int_cross_table_file" value="int_cross_table.parquet" ftype="parquet"/> |
| 104 | 120 |
| 105 <output name="recovered_feature_sample_table" ftype="parquet" | 121 <output name="recovered_feature_sample_table" ftype="parquet" |