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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@">
2 <description>annotate clustered features using a supplied MS1 database</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6
7 <expand macro="requirements"/>
8
9 <command detect_errors="exit_code"><![CDATA[
10 #set $computed_ppmthr = float($ppm) * 2
11 python3 '${__tool_directory__}/ipapy2_MS1_annotation.py'
12 --input_dataset_database '${mapped_isotope_patterns}' '${mapped_isotope_patterns.ext}'
13 --input_dataset_adducts '${all_adducts}' '${all_adducts.ext}'
14 --ppm ${ppm}
15 --ratiosd ${ratiosd}
16 #if $ppmunk
17 --ppmunk ${ppmunk}
18 #else
19 --ppmunk ${ppm}
20 #end if
21 --ratiounk ${ratiounk}
22 #if $ppmthr
23 --ppmthr ${ppmthr}
24 #else
25 --ppmthr ${computed_ppmthr}
26 #end if
27 --pRTNone ${pRTNone}
28 --pRTout ${pRTout}
29 --output_dataset '${MS1_annotations}' '${MS1_annotations.ext}'
30 --ncores \${GALAXY_SLOTS:-1}
31 ]]></command>
32
33 <inputs>
34 <param label="Mapped isotope patterns" name="mapped_isotope_patterns" type="data" format="csv,tsv,tabular,parquet" help="A dataset containing the MS1 data. Ideally obtained from map_isotope_patterns" />
35 <param label="all possible adducts" name="all_adducts" type="data" format="csv,tsv,tabular,parquet" help="A dataset containing the information on all the possible adducts given the database. Ideally obtained from compute_all_adducts" />
36 <expand macro="ppm"/>
37 <section name="unknown" title="settings for the identification of unknowns">
38 <expand macro="ms_unknown"/>
39 </section>
40 <section name="optional_settings" title="optional settings">
41 <expand macro="ms_options"/>
42 </section>
43 </inputs>
44
45 <outputs>
46 <data label="${tool.name} on ${on_string}" name="MS1_annotations" format_source="mapped_isotope_patterns"/>
47 </outputs>
48
49 <tests>
50 <test>
51 <param name="mapped_isotope_patterns" value="mapped_isotope_patterns.csv"/>
52 <param name="all_adducts" value="all_adducts.csv"/>
53 <param name="ppm" value="3"/>
54 <output name="MS1_annotations" file="MS1_annotations.csv" lines_diff="20"/>
55 </test>
56 </tests>
57
58 <help><![CDATA[
59
60 .. _ipapy2_ms1_annotation:
61
62 ==========================
63 ipaPy2 MS1 Annotation Tool
64 ==========================
65
66 **Tool Description**
67
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.
69
70 How it works
71 ------------
72
73 - **Prior probabilities** are calculated using only the mass information.
74 - **Posterior probabilities** incorporate mass, RT, prior knowledge, and isotope patterns for more accurate annotation.
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.
76
77 Inputs
78 ------
79
80 1. **Mapped isotope patterns**
81 Dataset containing MS1 data, ideally obtained from the ``map_isotope_patterns`` tool.
82
83 2. **All possible adducts**
84 Table listing all possible adducts for the database, ideally obtained from the ``compute_all_adducts`` tool.
85
86 3. **Parameters**
87 - **ppm**: Mass tolerance in parts per million for matching.
88 - **Unknown settings**: Parameters for handling unknowns, such as ppm and ratio thresholds.
89 - **Optional settings**: Additional parameters for advanced annotation control.
90
91 Outputs
92 -------
93
94 - **MS1_annotations**
95 Annotated dataset with additional columns describing the best-matching database entries, probabilities, and isotope pattern scores.
96
97 Example
98 -------
99
100 Suppose you have mapped isotope patterns and a list of all adducts. You can use this tool to annotate your features as follows:
101
102 .. code-block::
103
104 mapped_isotope_patterns.csv
105 all_adducts.csv
106
107 Set the desired tolerances (e.g., ``ppm = 3``) and run the tool. The output will be a table with annotations for each feature.
108
109 Notes
110 -----
111
112 - For best results, ensure your input files are correctly formatted and contain the required columns.
113 - The tool is designed to be flexible and can handle various input formats (CSV, TSV, Parquet, Tabular).
114
115 References
116 ----------
117
118 - For more details on the annotation algorithm and scoring, refer to the ipaPy2 documentation or associated publications.
119
120 ]]></help>
121
122 <expand macro="citations"/>
123 </tool>