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annotate plasmidtrakr.xml @ 8:17b409c9320d draft

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author galaxytrakr
date Wed, 29 Apr 2026 20:37:38 +0000
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1 <tool id="plasmidtrakr" name="Predict Isolate Source" version="0.1.6">
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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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9 <command detect_errors="exit_code"><![CDATA[
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10 python ${__tool_directory__}/predict_source.py
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11 -i '$mash_input'
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12 -b '$model_selection.path'
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13 -t '$threshold'
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14 -o '$prediction_output'
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15 ]]></command>
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16
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17 <inputs>
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18 <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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20 <param name="model_selection" type="select" label="Select Prediction Model" help="Choose which trained model to use for prediction.">
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21 <options from_data_table="plasmidtrakr_models">
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22 <validator type="no_options" message="No prediction models are configured. Please contact your Galaxy administrator." />
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23 </options>
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24 </param>
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26 <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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27 </inputs>
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29 <outputs>
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30 <data name="prediction_output" format="tabular" label="Prediction for ${on_string}" />
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31 </outputs>
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32
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33 <!-- FIXED: Cleaned up Markdown formatting in the help block (removed backslashes) -->
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34 <help><![CDATA[
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35 **What it does**
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36
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37 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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38
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39 **Workflow for Genome Assemblies**
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41 1. Go to the **mash screen** tool in Galaxy.
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42 2. In the **"Single or Paired-end reads"** dropdown, select **"Single"**.
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43 3. For the **"Select fastq dataset"** input, provide your **genome assembly FASTA file**.
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44 4. Run the `mash screen` job against the appropriate plasmid database.
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45 5. Use the tabular output from that job as the input for **this prediction tool**.
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46 6. Select the desired prediction model from the dropdown menu.
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47 7. Execute to get your prediction.
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48
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49 **Output**
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50
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51 A tabular file containing the isolate ID, the predicted source, and a confidence score.
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52 ]]></help>
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53
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54 <citations>
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55 <citation type="bibtex">
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56 @misc{strain_2026_plasmidtrakr,
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57 author = {Strain, Errol},
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58 title = {PlasmidTrakr: A tool for predicting isolate source from plasmid profiles},
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59 year = {2026},
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60 publisher = {GitHub},
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61 journal = {GitHub repository},
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62 howpublished = {\url{https://github.com/estrain/plasmidtrakr}}
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63 }
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64 </citation>
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65 </citations>
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66 </tool>