Mercurial > repos > recetox > recetox_aplcms_align_features
comparison recetox_aplcms_align_features.xml @ 4:a85b9670051c draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit ce3d81b59ef0895b61fcb1e17fa1553ccb28b077
| author | recetox |
|---|---|
| date | Wed, 03 May 2023 15:18:57 +0000 |
| parents | 1e2a13bcb5a7 |
| children | c44c73efd6e5 |
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| 3:1e2a13bcb5a7 | 4:a85b9670051c |
|---|---|
| 6 </macros> | 6 </macros> |
| 7 <expand macro="creator"/> | 7 <expand macro="creator"/> |
| 8 <expand macro="requirements"/> | 8 <expand macro="requirements"/> |
| 9 | 9 |
| 10 <command detect_errors="aggressive"><![CDATA[ | 10 <command detect_errors="aggressive"><![CDATA[ |
| 11 Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")' | 11 Rscript -e "cluster <- \${GALAXY_SLOTS:-1}" -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")' |
| 12 ]]></command> | 12 ]]></command> |
| 13 <configfiles> | 13 <configfiles> |
| 14 <configfile name="run_script"><![CDATA[ | 14 <configfile name="run_script"><![CDATA[ |
| 15 #set filenames = str("', '").join([str($f) for $f in $files]) | 15 #set filenames = str("', '").join([str($f) for $f in $files]) |
| 16 feature_tables <- load_parquet_collection(c('$filenames')) | 16 feature_tables <- load_parquet_collection(c('$filenames')) |
| 27 aligned_features <- create_aligned_feature_table( | 27 aligned_features <- create_aligned_feature_table( |
| 28 features_table = dplyr::bind_rows(feature_tables), | 28 features_table = dplyr::bind_rows(feature_tables), |
| 29 min_occurrence = $min_occurrence, | 29 min_occurrence = $min_occurrence, |
| 30 sample_names = sample_names, | 30 sample_names = sample_names, |
| 31 mz_tol_relative = get_mz_tol(tolerances), | 31 mz_tol_relative = get_mz_tol(tolerances), |
| 32 rt_tol_relative = get_rt_tol(tolerances) | 32 rt_tol_relative = get_rt_tol(tolerances), |
| 33 cluster = cluster | |
| 33 ) | 34 ) |
| 34 | 35 |
| 35 save_aligned_features(aligned_features, '$metadata_file', '$rt_file', '$intensity_file') | 36 save_aligned_features(aligned_features, '$metadata_file', '$rt_file', '$intensity_file') |
| 36 ]]></configfile> | 37 ]]></configfile> |
| 37 </configfiles> | 38 </configfiles> |