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comparison plasmidtrakr.xml @ 10:cbc924a737db draft

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planemo upload commit 17291695ca68c131f51a65367eb52e9b4c405532
author galaxytrakr
date Thu, 30 Apr 2026 00:48:20 +0000
parents c78b7a3494f9
children 6749dde97f01
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9:c78b7a3494f9 10:cbc924a737db
1 <tool id="plasmidtrakr" name="PlasmidTrakr" version="0.1.8"> 1 <tool id="plasmidtrakr" name="PlasmidTrakr" version="0.1.9">
2 <description>Predicts isolate source from plasmid profiles using a trained machine learning model</description> 2 <description>Predicts isolate source from plasmid profiles using a trained machine learning model</description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.5.3">pandas</requirement> 5 <requirement type="package" version="1.5.3">pandas</requirement>
6 <requirement type="package" version="1.2.2">scikit-learn</requirement> 6 <requirement type="package" version="1.2.2">scikit-learn</requirement>
7 </requirements> 7 </requirements>
8 8
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 python $__tool_directory__/predict_source.py 10 python $__tool_directory__/predict_source.py
11 -i '$mash_input' 11 -i $mash_input
12 -b '$model_selection.path' 12 -b $model_selection.fields.path
13 -t '$threshold' 13 -t $threshold
14 -o '$prediction_output' 14 -o $prediction_output
15 ]]></command> 15 ]]></command>
16 16
17 <inputs> 17 <inputs>
18 <param name="mash_input" type="data" format="tabular" label="Mash Screen Output" help="The tabular output file from the Galaxy 'mash screen' tool."/> 18 <param name="mash_input" type="data" format="tabular" label="Mash Screen Output" help="The tabular output file from the Galaxy 'mash screen' tool."/>
19 19
28 28
29 <outputs> 29 <outputs>
30 <data name="prediction_output" format="tabular" label="Prediction for ${on_string}" /> 30 <data name="prediction_output" format="tabular" label="Prediction for ${on_string}" />
31 </outputs> 31 </outputs>
32 32
33 <!-- FIXED: Cleaned up Markdown formatting in the help block (removed backslashes) -->
34 <help><![CDATA[ 33 <help><![CDATA[
35 **What it does** 34 **What it does**
36 35
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. 36 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.
38 37