Mercurial > repos > galaxytrakr > plasmidtrakr

comparison plasmidtrakr.xml @ 11:6749dde97f01 draft

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planemo upload commit b4bd359c36f6c12b50463fc92ca33865e61bf6b2
author galaxytrakr
date Thu, 30 Apr 2026 01:43:07 +0000
parents cbc924a737db
children c76b0b6f26cc
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10:cbc924a737db 11:6749dde97f01
1 <tool id="plasmidtrakr" name="PlasmidTrakr" version="0.1.9"> 1 <tool id="plasmidtrakr" name="PlasmidTrakr" version="0.1.10">
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.fields.path 12 -b $model_selection
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
20 <param name="model_selection" type="select" label="Select Prediction Model" help="Choose which trained model to use for prediction."> 20 <param name="model_selection" type="select" label="Select Prediction Model" help="Choose which trained model to use for prediction.">
21 <options from_data_table="plasmidtrakr_models"> 21 <options from_data_table="plasmidtrakr_models">
22 <column name="value" index="0"/>
23 <column name="name" index="1"/>
22 <validator type="no_options" message="No prediction models are configured. Please contact your Galaxy administrator." /> 24 <validator type="no_options" message="No prediction models are configured. Please contact your Galaxy administrator." />
23 </options> 25 </options>
24 </param> 26 </param>
25 27
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."/> 28 <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."/>