Mercurial > repos > recetox > recetox_aplcms_recover_weaker_signals

annotate recetox_aplcms_recover_weaker_signals.xml @ 12:24278c6b6d1c draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit f5e491b0f3f4005e3d8f75954f2d469297b300bf
author recetox
date Mon, 16 Sep 2024 15:17:59 +0000
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children
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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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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="annotation"/>
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8 <edam_operations>
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9 <edam_operation>operation_3215</edam_operation>
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10 <edam_operation>operation_3799</edam_operation>
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11 </edam_operations>
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12 <expand macro="refs"/>
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13 <expand macro="creator"/>
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14 <expand macro="requirements"/>
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16 <command detect_errors="aggressive"><![CDATA[
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17 python '${__tool_directory__}/mzml_id_getter.py' '$input_file';
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18 Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
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19 ]]></command>
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20 <configfiles>
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21 <configfile name="run_script"><![CDATA[
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22 sample_name <- readChar('sample_name.txt', file.info('sample_name.txt')\$size)
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24 if(is.na(sample_name)) {
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25 stop("The mzML file does not contain run ID.")
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26 }
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28 #set extracted_filenames = str("', '").join([str($f) for $f in $extracted_files])
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29 extracted_feature_tables <- load_parquet_collection(c('$extracted_filenames'))
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30 sample_names <- unlist(lapply(extracted_feature_tables, load_sample_name))
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31 validate_sample_names(sample_names)
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32 extracted_features <- select_table_with_sample_name(extracted_feature_tables, sample_name)
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33
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34 #set corrected_filenames = str("', '").join([str($f) for $f in $corrected_files])
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35 corrected_feature_tables <- load_parquet_collection(c('$corrected_filenames'))
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36 sample_names <- unlist(lapply(corrected_feature_tables, load_sample_name))
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37 validate_sample_names(sample_names)
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38 corrected_features <- select_table_with_sample_name(corrected_feature_tables, sample_name)
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40 metadata <- load_data_from_parquet_file('$metadata_file')
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41 rt_table <- load_data_from_parquet_file('$rt_file')
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42 intensity_table <- load_data_from_parquet_file('$intensity_file')
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44 recovered <- recover.weaker(
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45 filename = '$input_file',
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46 sample_name = sample_name,
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47 extracted_features = extracted_features,
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48 adjusted_features = corrected_features,
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49 metadata_table = metadata,
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50 rt_table = rt_table,
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51 intensity_table = intensity_table,
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52 mz_tol = $mz_tol/1e6,
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53 mz_tol_relative = $mz_tol_relative_ppm * 1e-06,
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54 rt_tol_relative = $rt_tol,
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55 #if $recover_mz_range:
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56 recover_mz_range = $recover_mz_range/1e6,
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57 #else:
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58 recover_mz_range = NA,
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59 #end if
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60 #if $recover_rt_range:
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61 recover_rt_range = $recover_rt_range,
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62 #else:
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63 recover_rt_range = NA,
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64 #end if
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65 use_observed_range = $use_observed_range,
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66 bandwidth = $bandwidth,
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67 #if $min_bandwidth:
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68 min_bandwidth = $min_bandwidth,
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69 #else:
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70 min_bandwidth = NA,
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71 #end if
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72 #if $max_bandwidth:
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73 max_bandwidth = $max_bandwidth,
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74 #else:
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75 max_bandwidth = NA,
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76 #end if
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77 recover_min_count = $recover_min_count,
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78 intensity_weighted = $intensity_weighted
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79 )
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80
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81 recovered <- select_adjusted(recovered)
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82
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83 recovered <- save_sample_name(recovered, sample_name)
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84 save_data_as_parquet_file(recovered, '$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[
2
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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>