Mercurial > repos > recetox > recetox_aplcms_recover_weaker_signals
annotate recetox_aplcms_recover_weaker_signals.xml @ 11:d7f5878a98c3 draft default tip
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b88eaca14b030fc0023989f3c83479e4975d172a
author | recetox |
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date | Thu, 01 Aug 2024 10:57:41 +0000 |
parents | a9bb2ccc53de |
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d7f5878a98c3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b88eaca14b030fc0023989f3c83479e4975d172a
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1 <tool id="recetox_aplcms_recover_weaker_signals" name="recetox-aplcms - recover weaker signals" version="@TOOL_VERSION@+galaxy0" profile="21.09"> |
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472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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2 <description>recover weaker signals from raw data using an aligned feature table</description> |
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067a308223e3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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3 <macros> |
067a308223e3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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4 <import>macros.xml</import> |
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472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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5 <import>help.xml</import> |
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067a308223e3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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6 </macros> |
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a9bb2ccc53de
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 97249a1af94ac5c387e1ede274dec5364f71cde9
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7 <expand macro="annotation"/> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
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8 <edam_operations> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
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9 <edam_operation>operation_3215</edam_operation> |
c3d4b82c7e5d
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
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10 <edam_operation>operation_3799</edam_operation> |
c3d4b82c7e5d
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 199dd33897bacaeb194ce9f5239cc4752c92e4df
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11 </edam_operations> |
9
a9bb2ccc53de
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 97249a1af94ac5c387e1ede274dec5364f71cde9
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12 <expand macro="refs"/> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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13 <expand macro="creator"/> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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14 <expand macro="requirements"/> |
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067a308223e3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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15 |
067a308223e3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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16 <command detect_errors="aggressive"><![CDATA[ |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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17 python '${__tool_directory__}/mzml_id_getter.py' '$input_file'; |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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18 Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")' |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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19 ]]></command> |
067a308223e3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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20 <configfiles> |
067a308223e3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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21 <configfile name="run_script"><![CDATA[ |
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472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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22 sample_name <- readChar('sample_name.txt', file.info('sample_name.txt')\$size) |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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23 |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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24 if(is.na(sample_name)) { |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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25 stop("The mzML file does not contain run ID.") |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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26 } |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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27 |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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28 #set extracted_filenames = str("', '").join([str($f) for $f in $extracted_files]) |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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29 extracted_feature_tables <- load_parquet_collection(c('$extracted_filenames')) |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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30 sample_names <- unlist(lapply(extracted_feature_tables, load_sample_name)) |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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31 validate_sample_names(sample_names) |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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32 extracted_features <- select_table_with_sample_name(extracted_feature_tables, sample_name) |
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067a308223e3
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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33 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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34 #set corrected_filenames = str("', '").join([str($f) for $f in $corrected_files]) |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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35 corrected_feature_tables <- load_parquet_collection(c('$corrected_filenames')) |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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36 sample_names <- unlist(lapply(corrected_feature_tables, load_sample_name)) |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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37 validate_sample_names(sample_names) |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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38 corrected_features <- select_table_with_sample_name(corrected_feature_tables, sample_name) |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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39 |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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40 metadata <- load_data_from_parquet_file('$metadata_file') |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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41 rt_table <- load_data_from_parquet_file('$rt_file') |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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42 intensity_table <- load_data_from_parquet_file('$intensity_file') |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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43 |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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44 recovered <- recover.weaker( |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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45 filename = '$input_file', |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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46 sample_name = sample_name, |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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47 extracted_features = extracted_features, |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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48 adjusted_features = corrected_features, |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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49 metadata_table = metadata, |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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50 rt_table = rt_table, |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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51 intensity_table = intensity_table, |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
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52 mz_tol = $mz_tol/1e6, |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 724ecb1b81ebd8a67488b8a9397177b2ff0357db
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53 mz_tol_relative = $mz_tol_relative_ppm * 1e-06, |
755ff0afaaff
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 724ecb1b81ebd8a67488b8a9397177b2ff0357db
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54 rt_tol_relative = $rt_tol, |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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55 #if $recover_mz_range: |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
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56 recover_mz_range = $recover_mz_range/1e6, |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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57 #else: |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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58 recover_mz_range = NA, |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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59 #end if |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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60 #if $recover_rt_range: |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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61 recover_rt_range = $recover_rt_range, |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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62 #else: |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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63 recover_rt_range = NA, |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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64 #end if |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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65 use_observed_range = $use_observed_range, |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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66 bandwidth = $bandwidth, |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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67 #if $min_bandwidth: |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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68 min_bandwidth = $min_bandwidth, |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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69 #else: |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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70 min_bandwidth = NA, |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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71 #end if |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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72 #if $max_bandwidth: |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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73 max_bandwidth = $max_bandwidth, |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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74 #else: |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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75 max_bandwidth = NA, |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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76 #end if |
472dc85ce7c5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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77 recover_min_count = $recover_min_count, |
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78 intensity_weighted = $intensity_weighted |
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79 ) |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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80 |
2
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81 recovered <- select_adjusted(recovered) |
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82 |
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83 recovered <- save_sample_name(recovered, sample_name) |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a
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84 save_data_as_parquet_file(recovered, '$output_file') |
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85 ]]></configfile> |
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86 </configfiles> |
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87 |
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88 <inputs> |
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89 <param name="input_file" type="data" format="mzml" label="Input spectra data" |
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90 help="Mass spectrometry sample-wise features table." /> |
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91 <param name="extracted_files" type="data_collection" collection_type="list" format="parquet" |
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92 label="Input extracted feature samples collection" help="Mass spectrometry files containing feature samples." /> |
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93 <param name="corrected_files" type="data_collection" collection_type="list" format="parquet" |
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94 label="Input corrected feature samples collection" help="Mass spectrometry file containing corrected feature samples." /> |
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95 <param name="metadata_file" type="data" format="parquet" label="Metadata table" |
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96 help="Peak metadata table from the align features step." /> |
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97 <param name="rt_file" type="data" format="parquet" label="RT table" |
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98 help="Table with retention times for features (rows) across samples (columns)." /> |
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99 <param name="intensity_file" type="data" format="parquet" label="Intensity table" |
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100 help="Table with intensities for features (rows) across samples (columns)." /> |
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101 <expand macro="tolerances"/> |
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102 <expand macro="recover_weaker_params"/> |
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103 <expand macro="bandwidth_params"/> |
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104 </inputs> |
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105 |
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106 <outputs> |
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107 <data label="${($input_file.element_identifier).rsplit('.',1)[0]}.parquet" name="output_file" format="parquet" /> |
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108 </outputs> |
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109 |
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110 <tests> |
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111 <test expect_failure="true" /> |
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112 </tests> |
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113 |
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114 <help> |
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115 <![CDATA[ |
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116 @RECOVER_WEAKER_SIGNALS_HELP@ |
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117 |
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118 @GENERAL_HELP@ |
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119 ]]> |
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120 </help> |
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121 |
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122 <expand macro="citations"/> |
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123 </tool> |