Mercurial > repos > recetox > recetox_aplcms_recover_weaker_signals

annotate recetox_aplcms_recover_weaker_signals.xml @ 3:c69a12bfc2fb draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4254c6f6f05915ceab5af5d7040ac2c44a8364b4
author recetox
date Mon, 03 Apr 2023 14:57:30 +0000
parents 472dc85ce7c5
children 755ff0afaaff
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1 <tool id="recetox_aplcms_recover_weaker_signals" name="recetox-aplcms - recover weaker signals" version="@TOOL_VERSION@+galaxy0">
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2 <description>recover weaker signals from raw data using an aligned feature table</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>help.xml</import>
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6 </macros>
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7 <expand macro="creator"/>
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8 <expand macro="requirements"/>
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10 <command detect_errors="aggressive"><![CDATA[
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11 python '${__tool_directory__}/mzml_id_getter.py' '$input_file';
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12 Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
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13 ]]></command>
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14 <configfiles>
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15 <configfile name="run_script"><![CDATA[
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16 sample_name <- readChar('sample_name.txt', file.info('sample_name.txt')\$size)
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18 if(is.na(sample_name)) {
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19 stop("The mzML file does not contain run ID.")
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20 }
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22 #set extracted_filenames = str("', '").join([str($f) for $f in $extracted_files])
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23 extracted_feature_tables <- load_parquet_collection(c('$extracted_filenames'))
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24 sample_names <- unlist(lapply(extracted_feature_tables, load_sample_name))
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25 validate_sample_names(sample_names)
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26 extracted_features <- select_table_with_sample_name(extracted_feature_tables, sample_name)
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28 #set corrected_filenames = str("', '").join([str($f) for $f in $corrected_files])
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29 corrected_feature_tables <- load_parquet_collection(c('$corrected_filenames'))
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30 sample_names <- unlist(lapply(corrected_feature_tables, load_sample_name))
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31 validate_sample_names(sample_names)
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32 corrected_features <- select_table_with_sample_name(corrected_feature_tables, sample_name)
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34 metadata <- load_data_from_parquet_file('$metadata_file')
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35 rt_table <- load_data_from_parquet_file('$rt_file')
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36 intensity_table <- load_data_from_parquet_file('$intensity_file')
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38 tolerances <- load_data_from_parquet_file('$tolerances')
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39
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40 recovered <- recover.weaker(
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41 filename = '$input_file',
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42 sample_name = sample_name,
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43 extracted_features = extracted_features,
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44 adjusted_features = corrected_features,
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45 metadata_table = metadata,
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46 rt_table = rt_table,
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47 intensity_table = intensity_table,
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48 mz_tol = $mz_tol/1e6,
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49 mz_tol_relative = get_mz_tol(tolerances),
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50 rt_tol_relative = get_rt_tol(tolerances),
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51 #if $recover_mz_range:
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52 recover_mz_range = $recover_mz_range/1e6,
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53 #else:
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54 recover_mz_range = NA,
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55 #end if
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56 #if $recover_rt_range:
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57 recover_rt_range = $recover_rt_range,
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58 #else:
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59 recover_rt_range = NA,
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60 #end if
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61 use_observed_range = $use_observed_range,
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62 bandwidth = $bandwidth,
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63 #if $min_bandwidth:
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64 min_bandwidth = $min_bandwidth,
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65 #else:
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66 min_bandwidth = NA,
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67 #end if
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68 #if $max_bandwidth:
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69 max_bandwidth = $max_bandwidth,
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70 #else:
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71 max_bandwidth = NA,
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72 #end if
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73 recover_min_count = $recover_min_count,
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74 intensity_weighted = $intensity_weighted
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75 )
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76
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77 recovered <- select_adjusted(recovered)
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78
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79 recovered <- save_sample_name(recovered, sample_name)
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80 save_data_as_parquet_file(recovered, '$output_file')
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81 ]]></configfile>
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82 </configfiles>
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84 <inputs>
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85 <param name="input_file" type="data" format="mzml" label="Input spectra data"
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86 help="Mass spectrometry sample-wise features table." />
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87 <param name="extracted_files" type="data_collection" collection_type="list" format="parquet"
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88 label="Input extracted feature samples collection" help="Mass spectrometry files containing feature samples." />
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89 <param name="corrected_files" type="data_collection" collection_type="list" format="parquet"
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90 label="Input corrected feature samples collection" help="Mass spectrometry file containing corrected feature samples." />
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91 <param name="metadata_file" type="data" format="parquet" label="Metadata table"
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92 help="Peak metadata table from the align features step." />
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93 <param name="rt_file" type="data" format="parquet" label="RT table"
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94 help="Table with retention times for features (rows) across samples (columns)." />
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95 <param name="intensity_file" type="data" format="parquet" label="Intensity table"
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96 help="Table with intensities for features (rows) across samples (columns)." />
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97 <param label="Input tolerances values" name="tolerances" type="data" format="parquet"
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98 help="Table containing tolerance values." />
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99 <expand macro="recover_weaker_params"/>
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100 <expand macro="bandwidth_params"/>
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101 </inputs>
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102
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103 <outputs>
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104 <data label="${tool.name} on ${on_string}" name="output_file" format="parquet" />
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105 </outputs>
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106
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107 <tests>
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108
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109 </tests>
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110
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111 <help>
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112 <![CDATA[
2
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113 @RECOVER_WEAKER_SIGNALS_HELP@
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114
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115 @GENERAL_HELP@
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116 ]]>
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117 </help>
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118
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119 <expand macro="citations"/>
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120 </tool>