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annotate plasmidtrakr.xml @ 3:6c88e978d6ad draft

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author galaxytrakr
date Wed, 29 Apr 2026 17:13:17 +0000
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1 <tool id="plasmidtrakr" name="Predict Isolate Source" version="0.1.1">
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2 <description>Predicts isolate source from plasmid profiles using a trained machine learning model</description>
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3
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4 <requirements>
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5 <requirement type="package" version="1.5.3">pandas</requirement>
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6 <requirement type="package" version="1.2.2">scikit-learn</requirement>
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7 </requirements>
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8
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9 <!-- FIXED: Added $ before __tool_directory__ -->
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10 <version_command>
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11 python '$__tool_directory__/predict_source.py' --version
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12 </version_command>
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13
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14 <!-- FIXED: Added $ before __tool_directory__ -->
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15 <command detect_errors="exit_code"><![CDATA[
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16 python '$__tool_directory__/predict_source.py'
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17 -i '$mash_input'
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18 -b '$model_selection.path'
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19 -t '$threshold'
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20 -o '$prediction_output'
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21 ]]></command>
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22
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23 <inputs>
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24 <param name="mash_input" type="data" format="tabular" label="Mash Screen Output" help="The tabular output file from the Galaxy 'mash screen' tool."/>
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25
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26 <param name="model_selection" type="select" label="Select Prediction Model" help="Choose which trained model to use for prediction.">
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27 <options from_data_table="plasmidtrakr_models">
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28 <validator type="no_options" message="No prediction models are configured. Please contact your Galaxy administrator." />
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29 </options>
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30 </param>
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31
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32 <param name="threshold" type="float" value="0.95" label="Mash Identity Threshold" help="Filter plasmid hits below this identity. Must match the threshold used for model training."/>
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33 </inputs>
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34
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35 <outputs>
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36 <data name="prediction_output" format="tabular" label="Prediction for ${on_string} using ${model_selection.name}" />
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37 </outputs>
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38
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39 <!-- FIXED: Cleaned up Markdown formatting in the help block (removed backslashes) -->
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40 <help><![CDATA[
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41 **What it does**
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42
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43 This tool takes the list of plasmid hits from the Galaxy **mash screen** tool and uses a pre-trained **machine learning model** to predict the original source of the isolate.
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44
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45 **Workflow for Genome Assemblies**
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46
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47 1. Go to the **mash screen** tool in Galaxy.
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48 2. In the **"Single or Paired-end reads"** dropdown, select **"Single"**.
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49 3. For the **"Select fastq dataset"** input, provide your **genome assembly FASTA file**.
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50 4. Run the `mash screen` job against the appropriate plasmid database.
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51 5. Use the tabular output from that job as the input for **this prediction tool**.
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52 6. Select the desired prediction model from the dropdown menu.
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53 7. Execute to get your prediction.
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54
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55 **Output**
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56
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57 A tabular file containing the isolate ID, the predicted source, and a confidence score.
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58 ]]></help>
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59
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60 <citations>
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61 <citation type="bibtex">
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62 @misc{strain_2026_plasmidtrakr,
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63 author = {Strain, Errol},
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64 title = {PlasmidTrakr: A tool for predicting isolate source from plasmid profiles},
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65 year = {2026},
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66 publisher = {GitHub},
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67 journal = {GitHub repository},
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68 howpublished = {\url{https://github.com/estrain/plasmidtrakr}}
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69 }
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70 </citation>
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71 </citations>
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72 </tool>