Mercurial > repos > recetox > recetox_aplcms_merge_known_table

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author recetox
date Thu, 31 Oct 2024 11:29:00 +0000
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1 <tool id="recetox_aplcms_merge_known_table" name="recetox-aplcms - merge known table" version="@TOOL_VERSION@+galaxy0" profile="21.09">
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2 <description>join knowledge from aligned features and known 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>
7
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7 <expand macro="annotation"/>
5
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8 <edam_operations>
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9 <edam_operation>operation_3436</edam_operation>
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10 </edam_operations>
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11 <expand macro="refs"/>
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12 <expand macro="creator"/>
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13 <expand macro="requirements"/>
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15 <command detect_errors="aggressive"><![CDATA[
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16 Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
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17 ]]></command>
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18 <configfiles>
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19 <configfile name="run_script"><![CDATA[
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20 metadata <- load_data_from_parquet_file('$metadata_file')
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21 rt_table <- load_data_from_parquet_file('$rt_file')
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22 intensity_table <- load_data_from_parquet_file('$intensity_file')
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23 known_table <- read_known_table('$known_table')
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25 feature_tables <- join_tables_to_list(metadata, rt_table, intensity_table)
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27 merged <- merge_features_and_known_table(
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28 features = feature_tables,
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29 known_table = known_table,
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30 #if $match_tol_ppm:
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31 match_tol_ppm = $match_tol_ppm,
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32 #else:
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33 match_tol_ppm = NA,
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34 #end if
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35 mz_tol_relative = $mz_tol_relative_ppm * 1e-06,
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36 rt_tol_relative = $rt_tol,
0
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37 #if $direction.selection == "TRUE":
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38 new_feature_min_count = $direction.new_feature_min_count,
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39 #end if
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40 from_features_to_known_table = $direction.selection
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41 )
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42
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43 #if $direction.selection == "TRUE":
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44 save_known_table(merged, '$output_known_table')
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45 save_pairing(merged, '$output_pairing')
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46 #else:
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47 save_aligned_features(merged, '$output_metadata_file', '$output_rt_file', '$output_intensity_file')
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48 #end if
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49 ]]></configfile>
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50 </configfiles>
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51
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52 <inputs>
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53 <param name="metadata_file" type="data" format="parquet" label="Metadata table"
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54 help="Peak metadata table from the align features step" />
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55 <param name="rt_file" type="data" format="parquet" label="RT table"
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56 help="Table with retention times for features (rows) across samples (columns)." />
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57 <param name="intensity_file" type="data" format="parquet" label="Intensity table"
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58 help="Table with intensities for features (rows) across samples (columns)." />
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59 <param label="Table of known features" name="known_table" type="data" format="parquet"
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60 help="A data table containing the known metabolite ions and previously found features. The table must
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61 contain these 18 columns: chemical_formula (optional), HMDB_ID (optional), KEGG_compound_ID (optional),
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62 neutral.mass (optional), ion.type (the ion form - optional), m.z (either theoretical or mean observed
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63 m/z value of previously found features), Number_profiles_processed (the total number of processed
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64 samples to build this database), Percent_found (the percentage of historically processed samples in
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65 which the feature appeared), mz_min (minimum observed m/z value), mz_max (maximum observed m/z value),
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66 RT_mean (mean observed retention time), RT_sd (standard deviation of observed retention time),
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67 RT_min (minimum observed retention time), RT_max (maximum observed retention time),
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68 int_mean.log. (mean observed log intensity), int_sd.log. (standard deviation of observed log intensity),
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69 int_min.log. (minimum observed log intensity), int_max.log. (maximum observed log intensity)." />
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70 <expand macro="tolerances"/>
0
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71
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72 <conditional name="direction">
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73 <param label="Tables merge direction" name="selection" type="select"
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74 help="Choose between merging feature to known_table and known_table to features.">
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75 <option value="TRUE">Merge features to known table</option>
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76 <option value="FALSE">Merge known table to features</option>
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77 </param>
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78 <when value="TRUE">
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79 <param name="new_feature_min_count" type="integer" value="2" min="1" label="Minimal occurence of feature"
0
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80 help="The minimum number of occurrences of a historically unseen (unknown) feature to add
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81 this feature into the database of known features." />
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82 </when>
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83 <when value="FALSE"></when>
0
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84 </conditional>
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85
6
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86 <param name="match_tol_ppm" type="integer" optional="true" min="0" label="Match tolerance [ppm]"
0
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87 help="The ppm tolerance to match identified features to known metabolites/features." />
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88 </inputs>
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89
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90 <outputs>
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91 <data name="output_metadata_file" format="parquet" label="${tool.name} on ${on_string} (metadata table)">
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92 <filter>direction['selection'] == 'FALSE'</filter>
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93 </data>
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94 <data name="output_rt_file" format="parquet" label="${tool.name} on ${on_string} (rt table)">
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95 <filter>direction['selection'] == 'FALSE'</filter>
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96 </data>
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97 <data name="output_intensity_file" format="parquet" label="${tool.name} on ${on_string} (intensity table)">
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98 <filter>direction['selection'] == 'FALSE'</filter>
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99 </data>
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100
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101 <data label="${tool.name} on ${on_string} (known table)" name="output_known_table" format="parquet" >
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102 <filter>direction['selection'] == 'TRUE'</filter>
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103 </data>
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104 <data label="${tool.name} on ${on_string} (pairing)" name="output_pairing" format="parquet" >
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105 <filter>direction['selection'] == 'TRUE'</filter>
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106 </data>
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107 </outputs>
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108
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109 <tests>
7
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110 <test expect_failure="true" />
0
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111 </tests>
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112
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113 <help>
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114 <![CDATA[
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115 @MERGE_KNOWN_TABLES_HELP@
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116
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117 @GENERAL_HELP@
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118 ]]>
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119 </help>
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120
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121 <expand macro="citations"/>
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122 </tool>