Mercurial > repos > recetox > recetox_aplcms_align_features

comparison recetox_aplcms_align_features.xml @ 4:dd9469db158b draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit ce3d81b59ef0895b61fcb1e17fa1553ccb28b077
author recetox
date Wed, 03 May 2023 15:16:23 +0000
parents d0b77b35819f
children 7bb4564d7b1a
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3:d0b77b35819f 4:dd9469db158b
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>