Mercurial > repos > recetox > ipapy2_ms1_annotation

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
author recetox
date Fri, 16 May 2025 08:00:41 +0000
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1 <tool id="ipapy2_MS1_annotation" name="ipaPy2 MS1 annotation" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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2 <description>annotate clustered features using a supplied MS1 database</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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7 <expand macro="requirements"/>
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8
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9 <command detect_errors="exit_code"><![CDATA[
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10 #set $computed_ppmthr = float($ppm) * 2
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11 python3 '${__tool_directory__}/ipapy2_MS1_annotation.py'
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12 --input_dataset_database '${mapped_isotope_patterns}' '${mapped_isotope_patterns.ext}'
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13 --input_dataset_adducts '${all_adducts}' '${all_adducts.ext}'
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14 --ppm ${ppm}
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15 --ratiosd ${ratiosd}
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16 #if $ppmunk
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17 --ppmunk ${ppmunk}
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18 #else
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19 --ppmunk ${ppm}
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20 #end if
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21 --ratiounk ${ratiounk}
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22 #if $ppmthr
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23 --ppmthr ${ppmthr}
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24 #else
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25 --ppmthr ${computed_ppmthr}
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26 #end if
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27 --pRTNone ${pRTNone}
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28 --pRTout ${pRTout}
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29 --output_dataset '${MS1_annotations}' '${MS1_annotations.ext}'
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30 --ncores \${GALAXY_SLOTS:-1}
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31 ]]></command>
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32
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33 <inputs>
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34 <param label="Mapped isotope patterns" name="mapped_isotope_patterns" type="data" format="csv,tsv,tabular,parquet" help="A dataset containing the MS1 data. Ideally obtained from map_isotope_patterns" />
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35 <param label="all possible adducts" name="all_adducts" type="data" format="csv,tsv,tabular,parquet" help="A dataset containing the information on all the possible adducts given the database. Ideally obtained from compute_all_adducts" />
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36 <expand macro="ppm"/>
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37 <section name="unknown" title="settings for the identification of unknowns">
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38 <expand macro="ms_unknown"/>
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39 </section>
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40 <section name="optional_settings" title="optional settings">
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41 <expand macro="ms_options"/>
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42 </section>
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43 </inputs>
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44
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45 <outputs>
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46 <data label="${tool.name} on ${on_string}" name="MS1_annotations" format_source="mapped_isotope_patterns"/>
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47 </outputs>
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48
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49 <tests>
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50 <test>
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51 <param name="mapped_isotope_patterns" value="mapped_isotope_patterns.csv"/>
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52 <param name="all_adducts" value="all_adducts.csv"/>
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53 <param name="ppm" value="3"/>
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54 <output name="MS1_annotations" file="MS1_annotations.csv" lines_diff="20"/>
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55 </test>
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56 </tests>
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58 <help><![CDATA[
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60 .. _ipapy2_ms1_annotation:
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61
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62 ==========================
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63 ipaPy2 MS1 Annotation Tool
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64 ==========================
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65
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66 **Tool Description**
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67
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68 This tool annotates clustered features in your dataset using MS1 information and a supplied adducts table. It calculates prior and posterior probabilities for each feature, leveraging mass, retention time (RT), chemical knowledge, and isotope patterns to provide high-confidence annotations.
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70 How it works
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71 ------------
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73 - **Prior probabilities** are calculated using only the mass information.
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74 - **Posterior probabilities** incorporate mass, RT, prior knowledge, and isotope patterns for more accurate annotation.
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75 - The tool matches features in your data to possible adducts and database entries, considering user-defined tolerances for mass (ppm) and other optional parameters.
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77 Inputs
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78 ------
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80 1. **Mapped isotope patterns**
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81 Dataset containing MS1 data, ideally obtained from the ``map_isotope_patterns`` tool.
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83 2. **All possible adducts**
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84 Table listing all possible adducts for the database, ideally obtained from the ``compute_all_adducts`` tool.
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85
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86 3. **Parameters**
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87 - **ppm**: Mass tolerance in parts per million for matching.
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88 - **Unknown settings**: Parameters for handling unknowns, such as ppm and ratio thresholds.
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89 - **Optional settings**: Additional parameters for advanced annotation control.
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90
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91 Outputs
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92 -------
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93
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94 - **MS1_annotations**
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95 Annotated dataset with additional columns describing the best-matching database entries, probabilities, and isotope pattern scores.
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96
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97 Example
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98 -------
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99
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100 Suppose you have mapped isotope patterns and a list of all adducts. You can use this tool to annotate your features as follows:
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101
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102 .. code-block::
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103
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104 mapped_isotope_patterns.csv
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105 all_adducts.csv
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106
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107 Set the desired tolerances (e.g., ``ppm = 3``) and run the tool. The output will be a table with annotations for each feature.
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108
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109 Notes
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110 -----
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111
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112 - For best results, ensure your input files are correctly formatted and contain the required columns.
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113 - The tool is designed to be flexible and can handle various input formats (CSV, TSV, Parquet, Tabular).
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114
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115 References
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116 ----------
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117
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118 - For more details on the annotation algorithm and scoring, refer to the ipaPy2 documentation or associated publications.
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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>