diff ipapy2_MS1_annotation.xml @ 0:7f84a8a5edde draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ipapy2_MS1_annotation.xml	Fri May 16 08:00:41 2025 +0000
@@ -0,0 +1,123 @@
+<tool id="ipapy2_MS1_annotation" name="ipaPy2 MS1 annotation" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+    <description>annotate clustered features using a supplied MS1 database</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    
+    <expand macro="requirements"/>
+
+    <command detect_errors="exit_code"><![CDATA[
+        #set $computed_ppmthr = float($ppm) * 2
+        python3  '${__tool_directory__}/ipapy2_MS1_annotation.py'
+        --input_dataset_database '${mapped_isotope_patterns}' '${mapped_isotope_patterns.ext}'
+        --input_dataset_adducts '${all_adducts}' '${all_adducts.ext}'
+        --ppm ${ppm}
+        --ratiosd ${ratiosd}
+        #if $ppmunk
+            --ppmunk ${ppmunk}
+        #else
+            --ppmunk ${ppm}
+        #end if
+        --ratiounk ${ratiounk}
+        #if $ppmthr
+            --ppmthr ${ppmthr}
+        #else
+            --ppmthr ${computed_ppmthr}
+        #end if
+        --pRTNone ${pRTNone}
+        --pRTout ${pRTout}
+        --output_dataset '${MS1_annotations}' '${MS1_annotations.ext}'
+        --ncores \${GALAXY_SLOTS:-1}
+    ]]></command>
+
+    <inputs>
+        <param label="Mapped isotope patterns" name="mapped_isotope_patterns" type="data" format="csv,tsv,tabular,parquet" help="A dataset containing the MS1 data. Ideally obtained from map_isotope_patterns" />
+        <param label="all possible adducts" name="all_adducts" type="data" format="csv,tsv,tabular,parquet" help="A dataset containing the information on all the possible adducts given the database. Ideally obtained from compute_all_adducts" />
+        <expand macro="ppm"/>
+        <section name="unknown" title="settings for the identification of unknowns">
+            <expand macro="ms_unknown"/>
+        </section>
+        <section name="optional_settings" title="optional settings">
+            <expand macro="ms_options"/>
+        </section>
+    </inputs>
+
+    <outputs>
+        <data label="${tool.name} on ${on_string}" name="MS1_annotations" format_source="mapped_isotope_patterns"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="mapped_isotope_patterns" value="mapped_isotope_patterns.csv"/>
+            <param name="all_adducts" value="all_adducts.csv"/>
+            <param name="ppm" value="3"/>
+            <output name="MS1_annotations" file="MS1_annotations.csv" lines_diff="20"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+
+.. _ipapy2_ms1_annotation:
+
+==========================
+ipaPy2 MS1 Annotation Tool
+==========================
+
+**Tool Description**
+
+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.
+
+How it works
+------------
+
+- **Prior probabilities** are calculated using only the mass information.
+- **Posterior probabilities** incorporate mass, RT, prior knowledge, and isotope patterns for more accurate annotation.
+- The tool matches features in your data to possible adducts and database entries, considering user-defined tolerances for mass (ppm) and other optional parameters.
+
+Inputs
+------
+
+1. **Mapped isotope patterns**  
+   Dataset containing MS1 data, ideally obtained from the ``map_isotope_patterns`` tool.
+
+2. **All possible adducts**  
+   Table listing all possible adducts for the database, ideally obtained from the ``compute_all_adducts`` tool.
+
+3. **Parameters**  
+   - **ppm**: Mass tolerance in parts per million for matching.
+   - **Unknown settings**: Parameters for handling unknowns, such as ppm and ratio thresholds.
+   - **Optional settings**: Additional parameters for advanced annotation control.
+
+Outputs
+-------
+
+- **MS1_annotations**  
+  Annotated dataset with additional columns describing the best-matching database entries, probabilities, and isotope pattern scores.
+
+Example
+-------
+
+Suppose you have mapped isotope patterns and a list of all adducts. You can use this tool to annotate your features as follows:
+
+.. code-block::
+
+    mapped_isotope_patterns.csv
+    all_adducts.csv
+
+Set the desired tolerances (e.g., ``ppm = 3``) and run the tool. The output will be a table with annotations for each feature.
+
+Notes
+-----
+
+- For best results, ensure your input files are correctly formatted and contain the required columns.
+- The tool is designed to be flexible and can handle various input formats (CSV, TSV, Parquet, Tabular).
+
+References
+----------
+
+- For more details on the annotation algorithm and scoring, refer to the ipaPy2 documentation or associated publications.
+
+    ]]></help>
+
+    <expand macro="citations"/>
+</tool>
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