Mercurial > repos > galaxytrakr > plasmidtrakr

annotate plasmidtrakr.xml @ 10:cbc924a737db draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 17291695ca68c131f51a65367eb52e9b4c405532
author galaxytrakr
date Thu, 30 Apr 2026 00:48:20 +0000
parents c78b7a3494f9
children 6749dde97f01
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
10
cbc924a737db planemo upload commit 17291695ca68c131f51a65367eb52e9b4c405532
galaxytrakr
parents: 9
diff changeset
1 <tool id="plasmidtrakr" name="PlasmidTrakr" version="0.1.9">
0
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
2 <description>Predicts isolate source from plasmid profiles using a trained machine learning model</description>
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
3
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
4 <requirements>
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
5 <requirement type="package" version="1.5.3">pandas</requirement>
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
6 <requirement type="package" version="1.2.2">scikit-learn</requirement>
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
7 </requirements>
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
8
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
9
c78b7a3494f9 planemo upload commit 117de6ae3eb1896dcb0044059b268136fc1b97ab
galaxytrakr
parents: 8
diff changeset
10 python $__tool_directory__/predict_source.py
10
cbc924a737db planemo upload commit 17291695ca68c131f51a65367eb52e9b4c405532
galaxytrakr
parents: 9
diff changeset
11 -i $mash_input
cbc924a737db planemo upload commit 17291695ca68c131f51a65367eb52e9b4c405532
galaxytrakr
parents: 9
diff changeset
12 -b $model_selection.fields.path
cbc924a737db planemo upload commit 17291695ca68c131f51a65367eb52e9b4c405532
galaxytrakr
parents: 9
diff changeset
13 -t $threshold
cbc924a737db planemo upload commit 17291695ca68c131f51a65367eb52e9b4c405532
galaxytrakr
parents: 9
diff changeset
14 -o $prediction_output
0
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
15 ]]></command>
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
16
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
17 <inputs>
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
18 <param name="mash_input" type="data" format="tabular" label="Mash Screen Output" help="The tabular output file from the Galaxy 'mash screen' tool."/>
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
19
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
20 <param name="model_selection" type="select" label="Select Prediction Model" help="Choose which trained model to use for prediction.">
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
21 <options from_data_table="plasmidtrakr_models">
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
22 <validator type="no_options" message="No prediction models are configured. Please contact your Galaxy administrator." />
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
23 </options>
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
24 </param>
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
25
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
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."/>
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
27 </inputs>
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
28
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
29 <outputs>
8
17b409c9320d planemo upload commit 8fe81cc450c2773ca4183b693341de07ff0337e9
galaxytrakr
parents: 7
diff changeset
30 <data name="prediction_output" format="tabular" label="Prediction for ${on_string}" />
0
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
31 </outputs>
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
32
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
33 <help><![CDATA[
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
34 **What it does**
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
35
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
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.
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
37
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
38 **Workflow for Genome Assemblies**
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
39
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
40 1. Go to the **mash screen** tool in Galaxy.
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
41 2. In the **"Single or Paired-end reads"** dropdown, select **"Single"**.
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
42 3. For the **"Select fastq dataset"** input, provide your **genome assembly FASTA file**.
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
43 4. Run the `mash screen` job against the appropriate plasmid database.
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
44 5. Use the tabular output from that job as the input for **this prediction tool**.
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
45 6. Select the desired prediction model from the dropdown menu.
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
46 7. Execute to get your prediction.
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
47
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
48 **Output**
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
49
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
50 A tabular file containing the isolate ID, the predicted source, and a confidence score.
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
51 ]]></help>
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
52
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
53 <citations>
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
54 <citation type="bibtex">
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
55 @misc{strain_2026_plasmidtrakr,
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
56 author = {Strain, Errol},
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
57 title = {PlasmidTrakr: A tool for predicting isolate source from plasmid profiles},
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
58 year = {2026},
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
59 publisher = {GitHub},
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
60 journal = {GitHub repository},
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
61 howpublished = {\url{https://github.com/estrain/plasmidtrakr}}
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
62 }
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
63 </citation>
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
64 </citations>
f25631df0e9f planemo upload commit 25e4c800a5358b8615dac18ea5e908e31c534020
galaxytrakr
parents:
diff changeset
65 </tool>