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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 174dafdf949ebf6e6d6f7a314db870daca8a46d6
author iuc
date Sat, 21 Jan 2023 13:49:27 +0000
parents 9ae55813ab79
children
comparison
equal deleted inserted replaced
0:9ae55813ab79 1:c9c60a241c7e
1 <tool id="PlasFlow" name="PlasFlow" version="1.0"> 1 <tool id="PlasFlow" name="PlasFlow" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
2 <description>Prediction of plasmid sequences in metagenomic contigs</description> 2 <description>Prediction of plasmid sequences in metagenomic contigs</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.1.0</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
3 <requirements> 7 <requirements>
4 <requirement type="package" version="1.1.0">plasflow</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">plasflow</requirement>
5 </requirements> 9 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 ## PlasFlow supports gz only partially
12 ## https://github.com/smaegol/PlasFlow/blob/45604ff637c65f709dabff63e665fa60896be241/PlasFlow.py#L444
13 #if $readFile.ext == "fasta.gz"
14 gunzip -c '$readFile' > 'reads.fasta' &&
15 #else
16 ln -s '$readFile' 'reads.fasta' &&
17 #end if
18
7 PlasFlow.py 19 PlasFlow.py
8 --input '$readFile' 20 --input 'reads.fasta'
9 --output 'output' 21 --output 'output'
10 --threshold '$threshold' 22 --threshold '$threshold'
11 ]]></command> 23 ]]></command>
12 <inputs> 24 <inputs>
13 <param name="readFile" type="data" format="fastq,fasta" optional="true" label="Sequence Reads" /> 25 <param name="readFile" type="data" format="fasta,fasta.gz" optional="true" label="Contig Sequences" />
14 <param argument="threshold" type="float" value="0.7" label="Threshold for porbability filtering"/> 26 <param argument="threshold" type="float" value="0.7" min="0" max="1" label="Threshold for probability filtering"/>
15 </inputs> 27 </inputs>
16 <outputs> 28 <outputs>
17 <data name="probability_table" from_work_dir="output" format="tabular" label="${tool.name} on ${on_string}: Probability table" /> 29 <data name="probability_table" from_work_dir="output" format="tabular" label="${tool.name} on ${on_string}: Probability table" />
18 <data name="chromosomes" from_work_dir="output_chromosomes.fasta" format="fasta" label="${tool.name} on ${on_string}: Chromosomes" /> 30 <data name="chromosomes" from_work_dir="output_chromosomes.fasta" format="fasta" label="${tool.name} on ${on_string}: Chromosomes" />
19 <data name="plasmids" from_work_dir="output_plasmids.fasta" format="fasta" label="${tool.name} on ${on_string}: Plasmids" /> 31 <data name="plasmids" from_work_dir="output_plasmids.fasta" format="fasta" label="${tool.name} on ${on_string}: Plasmids" />
20 <data name="unclassified" from_work_dir="output_unclassified.fasta" format="fasta" label="${tool.name} on ${on_string}: Unclassified" /> 32 <data name="unclassified" from_work_dir="output_unclassified.fasta" format="fasta" label="${tool.name} on ${on_string}: Unclassified" />
21 </outputs> 33 </outputs>
22 <tests> 34 <tests>
23 <test> 35 <test>
24 <param name="readFile" value="test.fasta"/> 36 <param name="readFile" value="test.fasta" ftype="fasta"/>
25 <param name="threshold" value="0.7"/> 37 <param name="threshold" value="0.7"/>
26 <output name="probability_table" value="output"/> 38 <output name="probability_table" value="output" compare="re_match"/>
39 <output name="chromosomes" value="output_chromosomes.fasta"/>
40 <output name="plasmids" value="output_plasmids.fasta"/>
41 <output name="unclassified" value="output_unclassified.fasta"/>
42 </test>
43 <test>
44 <param name="readFile" value="test.fasta.gz" ftype="fasta.gz"/>
45 <param name="threshold" value="0.7"/>
46 <output name="probability_table" value="output" compare="re_match"/>
27 <output name="chromosomes" value="output_chromosomes.fasta"/> 47 <output name="chromosomes" value="output_chromosomes.fasta"/>
28 <output name="plasmids" value="output_plasmids.fasta"/> 48 <output name="plasmids" value="output_plasmids.fasta"/>
29 <output name="unclassified" value="output_unclassified.fasta"/> 49 <output name="unclassified" value="output_unclassified.fasta"/>
30 </test> 50 </test>
31 </tests> 51 </tests>
32 <help><![CDATA[ 52 <help><![CDATA[
33 PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. It relies on the neural network models trained on full genome and plasmid sequences and is able to differentiate between plasmids and chromosomes with accuracy reaching 96%. It outperforms other available solutions for plasmids recovery from metagenomes and incorporates the thresholding which allows for exclusion of incertain predictions. PlasFlow has been published in Nucleic Acids Research 53 PlasFlow is a set of scripts used for prediction of plasmid sequences in
54 metagenomic contigs. It relies on the neural network models trained on full
55 genome and plasmid sequences and is able to differentiate between plasmids and
56 chromosomes with accuracy reaching 96%. It outperforms other available solutions
57 for plasmids recovery from metagenomes and incorporates the thresholding which
58 allows for exclusion of incertain predictions.
34 ]]></help> 59 ]]></help>
35 <citations> 60 <citations>
36 <citation type="doi">10.1093/nar/gkx1321</citation> 61 <citation type="doi">10.1093/nar/gkx1321</citation>
37 </citations> 62 </citations>
38 </tool> 63 </tool>