diff ipapy2_gibbs_sampler_add.xml @ 0:428abc41a101 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_gibbs_sampler_add.xml	Fri May 16 08:01:46 2025 +0000
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+<tool id="ipapy2_gibbs_sampler_add" name="ipaPy2 gibbs sampler additive" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    
+    <expand macro="requirements"/>
+
+    <command detect_errors="exit_code"><![CDATA[
+        python3 '${__tool_directory__}/ipapy2_gibbs_sampler_add.py'
+        --input_dataset_mapped_isotope_patterns '${mapped_isotope_patterns}' '${mapped_isotope_patterns.ext}'
+        --input_dataset_annotations '${annotations}' '${annotations.ext}'
+        --noits '${noits}'
+        --burn '${burn}'
+        --delta_add '${delta_add}'
+        --all_out '${all_out}'
+        #if $zs:
+            --zs '${zs}' '${zs.ext}'
+        #else:
+            --zs '' ''
+        #end if
+        #if $zs_out:
+            --zs_out '${zs_out}' '${zs_out.ext}'
+        #else:
+            --zs_out '' ''
+        #end if
+        --output_dataset '${annotations_out}' '${annotations_out.ext}'
+    ]]></command>
+
+    <inputs>
+        <expand macro="gibbs"/>
+        <param name="delta_add" type="float" value="1" min="0" label="adducts weight" help="parameter used when computing the conditional priors. The parameter must be positive. The smaller the parameter the more weight the adducts connections have on the posterior probabilities. Default 1." />
+    </inputs>
+
+    <outputs>
+        <data label="${tool.name} annotations on ${on_string}" name="annotations_out" format_source="mapped_isotope_patterns"/>
+        <data label="${tool.name} zs on ${on_string}" name="zs_out" format="txt">
+            <filter>options['all_out']</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <test  expect_num_outputs="2">
+            <param name="mapped_isotope_patterns" value="mapped_isotope_patterns.csv"/>
+            <param name="annotations" value="clean_annotations.csv"/>
+            <param name="noits" value="1000"/>
+            <param name="delta_add" value="0.1"/>
+            <!-- Not the best way to test, but the results are stochastic hence difficult to test-->
+            <output name="annotations_out">
+                <assert_contents>
+                    <has_n_columns n="15"  sep=","/>
+                    <has_n_lines n="15" delta="5" />
+                    <has_line line="id,name,formula,adduct,m/z,charge,RT range,ppm,isotope pattern score,fragmentation pattern score,prior,post,post Gibbs,chi-square pval,peak_id" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+
+.. _ipapy2_gibbs_sampler_add:
+
+=======================================
+ipaPy2 Gibbs Sampler Additive Tool
+=======================================
+
+**Tool Description**
+
+This tool implements a Gibbs sampler for the IPA (Integrated Probabilistic Annotation) model, focusing on additive (adducts-based) connections between features. It refines metabolite annotation probabilities by iteratively sampling from the posterior distribution, considering relationships between features that can be explained by known adduct transformations.
+
+How it works
+------------
+
+- The Gibbs sampler updates annotation probabilities by considering **adducts connections**: relationships between features that can be explained by known adduct transformations.
+- The influence of adducts connections is controlled by the ``adducts weight`` (`delta_add`) parameter: smaller values increase the influence of adducts connections on the posterior probabilities.
+- The process is stochastic, so results may vary between runs.
+- Optionally, the sampler can output the sampled states (`zs_out`) for further analysis.
+
+Inputs
+------
+
+1. **Mapped isotope patterns**  
+   Dataset containing mapped isotope patterns (e.g., output from the ipaPy2 map isotope patterns tool).
+
+2. **Annotations**  
+   Initial annotation table to be refined by the Gibbs sampler.
+
+3. **Number of iterations (`noits`)**  
+   Number of Gibbs sampler iterations to perform.
+
+4. **Burn-in (`burn`)**  
+   Number of initial iterations to discard (burn-in period).
+
+5. **Adducts weight (`delta_add`)**  
+   Parameter used when computing the conditional priors. Must be positive. The smaller the value, the more weight adducts connections have on the posterior probabilities (default: 1).
+
+6. **All out (`all_out`)**  
+   If enabled, outputs all intermediate results including sampled states.
+
+7. **zs**  
+   (Optional) Input file for initial state of the sampler.
+
+Outputs
+-------
+
+- **annotations_out**  
+  Refined annotation table with updated posterior probabilities.
+
+- **zs_out**  
+  (Optional) File containing sampled states from the Gibbs sampler (if `all_out` is enabled).
+
+Example
+-------
+
+Suppose you have mapped isotope patterns and an initial annotation table. You can run the Gibbs sampler as follows:
+
+.. code-block::
+
+    mapped_isotope_patterns.csv
+    clean_annotations.csv
+
+Set the number of iterations (e.g., ``noits = 1000``) and the adducts weight (e.g., ``delta_add = 0.1``), then run the tool. The output will be a refined annotation table and, optionally, a file with sampled states.
+
+Notes
+-----
+
+- The results are stochastic; repeated runs may yield slightly different outputs.
+- For best results, ensure all input files are correctly formatted and contain the required columns.
+- The tool supports multiple file formats (CSV, TSV, Parquet, Tabular) for flexibility.
+
+References
+----------
+
+- For more details on the Gibbs sampling algorithm and its application in metabolomics, refer to the ipaPy2 documentation or associated publications.
+
+    ]]></help>
+
+    <expand macro="citations"/>
+</tool>
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