Mercurial > repos > recetox > recetox_aplcms_two_step_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 10:11:13 +0000
parents bd044e7eebbd
children
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bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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1 <tool id="recetox_aplcms_two_step_hybrid" name="RECETOX apLCMS Two-Step Hybrid" version="@TOOL_VERSION@+galaxy0">
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2 <description>generate a feature table from LC/MS spectra of multi-batch experiments</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
1
886d52fd343f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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6 <expand macro="creator"/>
0
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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 $files])
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21
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22 two_step_hybrid_main(
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23 sample_files = c('$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 recovered_file = '${recovered_feature_sample_table}',
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27 aligned_file = '${aligned_feature_sample_table}',
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28 out_format = '$output_format.out_format',
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29 metadata = '${metadata}',
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30 cluster = as.integer(Sys.getenv('GALAXY_SLOTS', unset = 1)),
bd044e7eebbd planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit b3e0c34f12c9c38fb34bf48197974620d60b50c5
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31 min.within.batch.prop.detect = $multibatch_processing.min_within_batch_prop_detect,
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32 min.within.batch.prop.report = $multibatch_processing.min_within_batch_prop_detect,
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33 min.batch.prop = $multibatch_processing.min_batch_prop,
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34 batch.align.mz.tol = $multibatch_processing.batch_align_mz_tol,
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35 batch.align.chr.tol = $multibatch_processing.batch_align_chr_tol,
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36 min.pres = $noise_filtering.min_pres,
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37 min.run = $noise_filtering.min_run,
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38 mz.tol = $noise_filtering.mz_tol,
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39 baseline.correct.noise.percentile = $noise_filtering.baseline_correct_noise_percentile,
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40 baseline.correct = $noise_filtering.baseline_correct,
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41 intensity.weighted = $noise_filtering.intensity_weighted,
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42 shape.model = '$feature_detection.shape_model',
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43 peak.estim.method = '$feature_detection.peak_estim_method',
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44 BIC.factor = $feature_detection.BIC_factor,
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45 min.bw = $feature_detection.min_bandwidth,
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46 max.bw = $feature_detection.max_bandwidth,
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47 sd.cut = c($feature_detection.sd_cut_min, $feature_detection.sd_cut_max),
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48 sigma.ratio.lim = c($feature_detection.sigma_ratio_lim_min, $feature_detection.sigma_ratio_lim_max),
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49 component.eliminate = $feature_detection.component_eliminate,
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50 moment.power = $feature_detection.moment_power,
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51 align.mz.tol = $peak_alignment.align_mz_tol,
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52 align.chr.tol = $peak_alignment.align_chr_tol,
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53 max.align.mz.diff = $peak_alignment.max_align_mz_diff,
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54 recover.mz.range = $weak_signal_recovery.recover_mz_range,
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55 recover.chr.range = $weak_signal_recovery.recover_chr_range,
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56 use.observed.range = $weak_signal_recovery.use_observed_range,
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57 recover.min.count = $weak_signal_recovery.recover_min_count,
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58 match.tol.ppm = $history_db.match_tol_ppm,
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59 new.feature.min.count = $history_db.new_feature_min_count
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60 )
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61 ]]></configfile>
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62 </configfiles>
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63
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64 <expand macro="inputs">
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65 <param name="metadata" type="data" format="csv" label="metadata" help="A csv table with two columns, where the first column contains sample names and the second batch labels for each sample."/>
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66 <expand macro="history_db"/>
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67 <expand macro="noise_filtering" />
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68 <expand macro="feature_detection"/>
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69 <expand macro="peak_alignment"/>
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70 <expand macro="weak_signal_recovery"/>
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71 <expand macro="multibatch_processing"/>
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72 <expand macro="output_format"/>
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73 </expand>
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74
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75 <outputs>
1
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76 <expand macro="unsupervised_outputs">
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77 <data name="updated_known_table" format="parquet" label="${tool.name} updated_known_table on ${on_string}"/>
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78 </expand>
0
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79 </outputs>
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80
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81 <tests>
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82 <test>
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83 <param name="known_table" value="known_table.parquet" ftype="parquet"/>
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84 <param name="files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml,mbr_test0_copy.mzml" ftype="mzml"/>
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85 <param name="metadata" value="two_step_hybrid_info.csv" ftype="csv"/>
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86 <param name="moment_power" value="2"/>
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87 <param name="sd_cut_max" value="100"/>
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88 <param name="sd_cut_min" value="0.1"/>
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89 <param name="sigma_ratio_lim_max" value="20"/>
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90 <param name="sigma_ratio_lim_min" value="0.05"/>
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91 <section name="output_format">
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92 <param name="out_format" value="recetox"/>
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93 </section>
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94 <output name="recovered_feature_sample_table" file="two_step_hybrid.recetox.parquet" ftype="parquet"/>
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95 </test>
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96 </tests>
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97
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98 <help>
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99 <![CDATA[
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100 @HELP_two-step-hybrid@
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101 ]]>
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102 </help>
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103
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104 <expand macro="citations">
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105 <citation type="doi">10.1038/s41598-020-70850-0</citation>
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106 </expand>
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107 </tool>