Mercurial > repos > recetox > recetox_aplcms_recover_weaker_signals

annotate recetox_aplcms_recover_weaker_signals.xml @ 0:067a308223e3 draft

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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 10:18:24 +0000
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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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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 LC/MS spectra</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>macros_split.xml</import>
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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7 <expand macro="creator"/>
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8
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9 <expand macro="requirements"/>
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10 <command detect_errors="aggressive"><![CDATA[
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11 sh ${symlink_inputs} &&
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12 Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${__tool_directory__}/main.R")' -e 'source("${run_script}")'
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13 ]]></command>
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14 <configfiles>
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15 <configfile name="symlink_inputs">
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16 #for $infile in $ms_files
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17 ln -s '${infile}' '${infile.element_identifier}'
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18 #end for
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19 #for $infile in $extracted_files
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20 ln -s '${infile}' '${infile.element_identifier}'
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21 #end for
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22 #for $infile in $corrected_files
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23 ln -s '${infile}' '${infile.element_identifier}'
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24 #end for
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25 </configfile>
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26 <configfile name="run_script"><![CDATA[
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27 #set filenames = str("', '").join([str($f.element_identifier) for $f in $ms_files])
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28 filenames <- sort_samples_by_acquisition_number(c('$filenames'))
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29
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30 #set extracted_files = str("', '").join([str($f.element_identifier) for $f in $extracted_files])
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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31 extracted <- load_features(c('$extracted_files'))
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32
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33 #set corrected_files = str("', '").join([str($f.element_identifier) for $f in $corrected_files])
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34 corrected <- load_features(c('$corrected_files'))
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36 aligned <- load_aligned_features('$rt_cross_table_file', '$int_cross_table_file', '$tolerances_file')
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37
067a308223e3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 19de0924a65bc65cbbf7c1fc17e9b5348305f95c
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38 cluster <- as.integer(Sys.getenv('GALAXY_SLOTS', unset = 1))
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40 recovered <- recover_signals(cluster,
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41 filenames,
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42 extracted,
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43 corrected,
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44 aligned,
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45 $mz_tol,
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46 $weak_signal_recovery.recover_mz_range,
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47 $weak_signal_recovery.recover_chr_range,
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48 $weak_signal_recovery.use_observed_range,
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49 $min_bandwidth,
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50 $max_bandwidth,
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51 $weak_signal_recovery.recover_min_count
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52 )
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53
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54 aligned_feature_sample_table <- create_feature_sample_table(aligned)
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55 recovered_feature_sample_table <- create_feature_sample_table(recovered)
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56
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57 save_all_features(recovered, filenames)
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58 save_all_feature_tables(aligned_feature_sample_table, recovered_feature_sample_table,
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59 '${aligned_feature_sample_table}', '${recovered_feature_sample_table}',
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60 '$output_format.out_format')
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61 ]]></configfile>
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62 </configfiles>
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63
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64 <inputs>
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65 <param name="ms_files" type="data" format="mzdata,mzml,mzxml,netcdf" multiple="true" min="2" label="Input data"
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66 help="Mass spectrometry file for peak extraction." />
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67 <param name="extracted_files" type="data" format="parquet" multiple="true" min="2" label="Input extracted feature samples"
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68 help="Mass spectrometry files containing feature samples." />
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69 <param name="corrected_files" type="data" format="parquet" multiple="true" min="2" label="Input corrected feature samples"
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70 help="Mass spectrometry file containing corrected feature samples." />
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71 <param name="tolerances_file" type="data" format="parquet" label="Input tolerances" help="TBD"/>
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72 <param name="rt_cross_table_file" type="data" format="parquet" label="Input rt cross table" help="TBD"/>
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73 <param name="int_cross_table_file" type="data" format="parquet" label="Input int cross table" help="TBD"/>
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74 <expand macro="mz_tol_macro"/>
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75 <param name="min_bandwidth" type="float" optional="true" label="min_bandwidth (optional)"
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76 help="The minimum bandwidth to use in the kernel smoother." />
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77 <param name="max_bandwidth" type="float" optional="true" label="max_bandwidth (optional)"
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78 help="The maximum bandwidth to use in the kernel smoother." />
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79 <expand macro="weak_signal_recovery"/>
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80 <expand macro="output_format"/>
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81 </inputs>
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82
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83 <outputs>
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84 <expand macro="unsupervised_outputs">
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85 <collection name="extracted_features" type="list" label="${tool.name} extracted_features on ${on_string}">
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86 <discover_datasets pattern="__designation__" directory="extracted" format="parquet" />
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87 </collection >
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88 <collection name="corrected_features" type="list" label="${tool.name} corrected_features on ${on_string}">
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89 <discover_datasets pattern="__designation__" directory="corrected" format="parquet" />
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90 </collection >
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91 </expand>
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92 </outputs>
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93
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94 <tests>
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95 <test>
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96 <param name="ms_files" value="mbr_test2.mzml,mbr_test1.mzml,mbr_test0.mzml" ftype="mzml"/>
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97 <param name="extracted_files" ftype="parquet"
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98 value="extracted_expected/extracted_0.parquet,extracted_expected/extracted_1.parquet,extracted_expected/extracted_2.parquet"/>
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99 <param name="corrected_files" ftype="parquet"
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100 value="corrected_expected/corrected_0.parquet,corrected_expected/corrected_1.parquet,corrected_expected/corrected_2.parquet"/>
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101 <param name="tolerances_file" value="tolerances.parquet" ftype="parquet"/>
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102 <param name="rt_cross_table_file" value="rt_cross_table.parquet" ftype="parquet"/>
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103 <param name="int_cross_table_file" value="int_cross_table.parquet" ftype="parquet"/>
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104
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105 <output name="recovered_feature_sample_table" ftype="parquet"
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106 file="unsupervised_output/unsupervised_recovered_feature_sample_table.parquet"/>
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107 <output name="aligned_feature_sample_table" ftype="parquet"
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108 file="unsupervised_output/unsupervised_aligned_feature_sample_table.parquet"/>
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109 <output_collection name="corrected_features" type="list">
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110 <element name="mbr_test0.parquet" file="unsupervised_output/corrected_features_0.parquet" ftype="parquet"/>
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111 <element name="mbr_test1.parquet" file="unsupervised_output/corrected_features_1.parquet" ftype="parquet"/>
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112 <element name="mbr_test2.parquet" file="unsupervised_output/corrected_features_2.parquet" ftype="parquet"/>
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113 </output_collection>
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114 <output_collection name="extracted_features" type="list">
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115 <element name="mbr_test0.parquet" file="unsupervised_output/extracted_features_0.parquet" ftype="parquet"/>
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116 <element name="mbr_test1.parquet" file="unsupervised_output/extracted_features_1.parquet" ftype="parquet"/>
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117 <element name="mbr_test2.parquet" file="unsupervised_output/extracted_features_2.parquet" ftype="parquet"/>
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118 </output_collection>
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119 </test>
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120 </tests>
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121
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122 <help>
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123 <![CDATA[
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124 This is a tool which runs apLCMS recovery of weaker signals.
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125
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126 @GENERAL_HELP@
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127 ]]>
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128 </help>
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129
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130 <expand macro="citations"/>
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131 </tool>