Mercurial > repos > recetox > recetox_aplcms_hybrid

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
author recetox
date Fri, 10 Jun 2022 10:10:32 +0000
parents 5bb20231a48a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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8ff3d8d21333 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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1 <tool id="recetox_aplcms_hybrid" name="RECETOX apLCMS Hybrid" version="@TOOL_VERSION@+galaxy3">
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2 <description>generate a feature table from LC/MS spectra</description>
c2213632ca71 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit accce68183c78552905b4446a8cab581911275ef"
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3 <macros>
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4 <import>macros.xml</import>
4
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5 </macros>
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6 <expand macro="creator"/>
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8 <expand macro="requirements"/>
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9 <command detect_errors="aggressive"><![CDATA[
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10 sh ${symlink_inputs} &&
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11 Rscript -e 'source("${__tool_directory__}/main.R")' -e 'source("${run_script}")'
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12 ]]></command>
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13 <configfiles>
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14 <configfile name="symlink_inputs">
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15 #for $infile in $files
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16 ln -s '${infile}' '${infile.element_identifier}'
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17 #end for
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18 </configfile>
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19 <configfile name="run_script"><![CDATA[
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20 #set filenames_str = str("', '").join([str($f.element_identifier) for $f in $files])
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22 hybrid_main(
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23 sample_files = c('$filenames_str'),
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24 known_table_file = '${known_table}',
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25 updated_known_table_file = '${updated_known_table}',
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26 pairing_file = '${feature_known_table_pairing}',
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27 aligned_file = '${aligned_feature_sample_table}',
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28 recovered_file = '${recovered_feature_sample_table}',
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29 out_format = '$output_format.out_format',
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30 min_exp = $noise_filtering.min_exp,
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31 min_pres = $noise_filtering.min_pres,
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32 min_run = $noise_filtering.min_run,
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33 mz_tol = $noise_filtering.mz_tol,
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34 baseline_correct = $noise_filtering.baseline_correct,
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35 baseline_correct_noise_percentile = $noise_filtering.baseline_correct_noise_percentile,
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36 intensity_weighted = $noise_filtering.intensity_weighted,
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37 shape_model = '$feature_detection.shape_model',
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38 BIC_factor = $feature_detection.BIC_factor,
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39 peak_estim_method = '$feature_detection.peak_estim_method',
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40 min_bandwidth = $feature_detection.min_bandwidth,
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41 max_bandwidth = $feature_detection.max_bandwidth,
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42 sd_cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max),
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43 sigma_ratio_lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max),
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44 component_eliminate = $feature_detection.component_eliminate,
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45 moment_power = $feature_detection.moment_power,
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46 align_chr_tol = $peak_alignment.align_chr_tol,
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47 align_mz_tol = $peak_alignment.align_mz_tol,
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48 max_align_mz_diff = $peak_alignment.max_align_mz_diff,
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49 match_tol_ppm = $history_db.match_tol_ppm,
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50 new_feature_min_count = $history_db.new_feature_min_count,
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51 recover_mz_range = $weak_signal_recovery.recover_mz_range,
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52 recover_chr_range = $weak_signal_recovery.recover_chr_range,
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53 use_observed_range = $weak_signal_recovery.use_observed_range,
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54 recover_min_count = $weak_signal_recovery.recover_min_count,
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55 cluster = as.integer(Sys.getenv('GALAXY_SLOTS', unset = 1))
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56 )
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57 ]]></configfile>
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58 </configfiles>
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59
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60 <expand macro="inputs">
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61 <expand macro="history_db"/>
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62 <expand macro="noise_filtering">
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63 <param name="min_exp" type="integer" min="1" value="2"
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64 label="min_exp"
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65 help="If a feature is to be included in the final feature table, it must be present in at least this number of samples." />
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66 </expand>
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67 <expand macro="feature_detection"/>
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68 <expand macro="peak_alignment"/>
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69 <expand macro="weak_signal_recovery"/>
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70 <expand macro="output_format"/>
4
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71 </expand>
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72
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73 <outputs>
13
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74 <expand macro="unsupervised_outputs">
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75 <collection name="extracted_features" type="list" label="${tool.name} extracted_features on ${on_string}">
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76 <discover_datasets pattern="__designation__" directory="extracted" format="parquet" />
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77 </collection >
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78 <collection name="corrected_features" type="list" label="${tool.name} corrected_features on ${on_string}">
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79 <discover_datasets pattern="__designation__" directory="corrected" format="parquet" />
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80 </collection >
14
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81 <data name="updated_known_table" format="parquet" label="${tool.name} updated_known_table on ${on_string}"/>
13
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82 </expand>
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83 <data name="feature_known_table_pairing" format="tabular"
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84 label="${tool.name} feature_known_table_pairing on ${on_string}" hidden="true"/>
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85 </outputs>
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86
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87 <tests>
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88 <test>
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89 <param name="known_table" value="known_table.parquet" ftype="parquet"/>
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90 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/>
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91 <output name="recovered_feature_sample_table" file="hybrid_recovered_feature_sample_table.parquet"
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92 ftype="parquet"/>
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93 </test>
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94 <test>
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95 <param name="known_table" value="known_table.parquet" ftype="parquet"/>
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96 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/>
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97 <section name="output_format">
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98 <param name="out_format" value="recetox"/>
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99 </section>
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100 <output name="recovered_feature_sample_table" file="hybrid.recetox.parquet" ftype="parquet"/>
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101 </test>
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102 </tests>
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103
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104 <help>
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105 <![CDATA[
ab2b7948bdb7 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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106 @HELP_hybrid@
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107 ]]>
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108 </help>
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109
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110 <expand macro="citations"/>
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111 </tool>