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author recetox
date Mon, 12 May 2025 14:05:37 +0000
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1 <tool id="target_screen" name="MS Target Screening" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
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2 <description>Extract peaks from recetox-aplcms tables using a list of target ions</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.1.0</token>
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5 <token name="@VERSION_SUFFIX@">1</token>
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6 </macros>
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8 <requirements>
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9 <requirement type="package" version="2.2.3">pandas</requirement>
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10 <requirement type="package" version="17.0.0">pyarrow</requirement>
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11 </requirements>
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13 <command detect_errors="exit_code"><![CDATA[
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14 python3 '${__tool_directory__}/target_screen.py' --peaks '$peaks' '$peaks.ext' --markers '$markers' '$markers.ext' --output '$hits' --ppm $ppm --rt_tol $rt
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15 ]]></command>
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17 <inputs>
1
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18 <param name="peaks" type="data" format="parquet,tabular,tsv,csv" label="Peaks Table" help="Input table containing detected peaks in Parquet format. Each row should represent a peak with columns for m/z, retention time, and intensity." />
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19 <param name="markers" type="data" format="parquet,tabular,tsv,csv" label="Target Markers Table" help="Input table containing target markers in tabular format. Each row should represent a marker with columns for m/z and retention time." />
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20 <param name="ppm" type="integer" min="0" max="1000" value="10" label="Mass Tolerance (ppm)" help="Tolerance for filtering peaks based on mass-to-charge ratio (m/z) in parts per million (ppm). The tolerance is applied symmetrically (±), so a value of 10 will match peaks within ±10 ppm of the target m/z." />
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21 <param name="rt" type="integer" min="0" max="100" value="10" label="Retention Time Tolerance" help="Tolerance for filtering peaks based on retention time in the same units as the input data. The tolerance is applied symmetrically (±), so a value of 10 will match peaks within ±10 units of the target retention time." />
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22 </inputs>
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24 <outputs>
1
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25 <data name="hits" format="tabular" label="Filtered Peaks (${tool.name} on ${on_string})" />
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26 </outputs>
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28 <tests>
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29 <test>
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30 <param name="peaks" value="target_screen/peaks.parquet"/>
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31 <param name="markers" value="target_screen/markers.tsv"/>
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32 <output name="hits" value="target_screen/out.tsv"/>
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33 </test>
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34 </tests>
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35 <help><![CDATA[
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37 .. class:: infomark
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38
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39 **What it does**
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40
1
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41 This tool extracts peaks from a table of detected peaks based on a list of target markers. Peaks are matched to markers using a specified tolerance for mass-to-charge ratio (ppm) and retention time. Both tolerances are applied symmetrically (±). For example, if the retention time tolerance is set to 10, peaks within ±10 units of the target retention time will be matched.
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42
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43 **Inputs**
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44
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45 1. **Peaks Table (Parquet Format)**:
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46 A table containing detected peaks. The table should be in Parquet format and include the following columns:
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47
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48 - `mz`: Mass-to-charge ratio (m/z) of the peak.
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49 - `rt`: Retention time of the peak.
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50 - `intensity`: Intensity of the peak.
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51
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52 Example Peaks Table:
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54 .. list-table:: Example Peaks Table
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55 :header-rows: 1
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57 * - mz
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58 - rt
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59 - intensity
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60 * - 100.123
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61 - 5.2
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62 - 1500
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63 * - 200.456
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64 - 10.5
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65 - 3000
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66
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67 2. **Target Markers Table (Tabular Format)**:
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68 A table containing target markers. The table should be in tabular format and include the following columns:
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69
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70 - `mz`: Mass-to-charge ratio (m/z) of the marker.
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71 - `rt`: Retention time of the marker.
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72
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73 Example Markers Table:
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74
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75 .. list-table:: Example Markers Table
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76 :header-rows: 1
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78 * - mz
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79 - rt
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80 * - 100.123
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81 - 5.2
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82 * - 200.456
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83 - 10.5
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84
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85 **Parameters**
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86
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87 - **Mass Tolerance (ppm)**:
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88 The tolerance for matching peaks to markers based on their mass-to-charge ratio (m/z). The value is specified in parts per million (ppm). The tolerance is applied symmetrically (±), so a value of 10 will match peaks within ±10 ppm of the target m/z.
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89
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90 - **Retention Time Tolerance**:
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91 The tolerance for matching peaks to markers based on their retention time. The value is specified in the same units as the input data. The tolerance is applied symmetrically (±), so a value of 10 will match peaks within ±10 units of the target retention time.
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92
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93 **Outputs**
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94
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95 - **Filtered Peaks Table**:
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96 A tabular file containing the peaks that matched the target markers based on the specified tolerances.
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97
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98 **Example Usage**
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99
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100 This tool can be used to filter peaks from a mass spectrometry dataset based on a list of known target markers, enabling targeted analysis of specific compounds.
0
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101 ]]></help>
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102 <citations>
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103 <citation type="doi">10.25080/Majora-92bf1922-00a</citation>
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104 </citations>
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105 </tool>