annotate plasflow.xml @ 2:1d2a91ab28b7 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 469db427c69fa33e2e0acf042d8a52f552551261
author iuc
date Mon, 11 Mar 2024 15:13:13 +0000
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1 <tool id="PlasFlow" name="PlasFlow" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
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2 <description>Prediction of plasmid sequences in metagenomic contigs</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.1.0</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <xrefs>
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8 <xref type="bio.tools">plasflow</xref>
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9 </xrefs>
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10 <requirements>
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11 <requirement type="package" version="@TOOL_VERSION@">plasflow</requirement>
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12 </requirements>
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13 <command detect_errors="exit_code"><![CDATA[
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14 ## PlasFlow supports gz only partially
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15 ## https://github.com/smaegol/PlasFlow/blob/45604ff637c65f709dabff63e665fa60896be241/PlasFlow.py#L444
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16 #if $readFile.ext == "fasta.gz"
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17 gunzip -c '$readFile' > 'reads.fasta' &&
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18 #else
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19 ln -s '$readFile' 'reads.fasta' &&
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20 #end if
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21
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22 PlasFlow.py
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23 --input 'reads.fasta'
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24 --output 'output'
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25 --threshold '$threshold'
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26 ]]></command>
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27 <inputs>
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28 <param name="readFile" type="data" format="fasta,fasta.gz" optional="true" label="Contig Sequences" />
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29 <param argument="threshold" type="float" value="0.7" min="0" max="1" label="Threshold for probability filtering"/>
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30 </inputs>
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31 <outputs>
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32 <data name="probability_table" from_work_dir="output" format="tabular" label="${tool.name} on ${on_string}: Probability table" />
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33 <data name="chromosomes" from_work_dir="output_chromosomes.fasta" format="fasta" label="${tool.name} on ${on_string}: Chromosomes" />
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34 <data name="plasmids" from_work_dir="output_plasmids.fasta" format="fasta" label="${tool.name} on ${on_string}: Plasmids" />
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35 <data name="unclassified" from_work_dir="output_unclassified.fasta" format="fasta" label="${tool.name} on ${on_string}: Unclassified" />
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="readFile" value="test.fasta" ftype="fasta"/>
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40 <param name="threshold" value="0.7"/>
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41 <output name="probability_table" value="output" compare="re_match"/>
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42 <output name="chromosomes" value="output_chromosomes.fasta"/>
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43 <output name="plasmids" value="output_plasmids.fasta"/>
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44 <output name="unclassified" value="output_unclassified.fasta"/>
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45 </test>
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46 <test>
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47 <param name="readFile" value="test.fasta.gz" ftype="fasta.gz"/>
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48 <param name="threshold" value="0.7"/>
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49 <output name="probability_table" value="output" compare="re_match"/>
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50 <output name="chromosomes" value="output_chromosomes.fasta"/>
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51 <output name="plasmids" value="output_plasmids.fasta"/>
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52 <output name="unclassified" value="output_unclassified.fasta"/>
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53 </test>
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54 </tests>
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55 <help><![CDATA[
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56 PlasFlow is a set of scripts used for prediction of plasmid sequences in
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57 metagenomic contigs. It relies on the neural network models trained on full
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58 genome and plasmid sequences and is able to differentiate between plasmids and
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59 chromosomes with accuracy reaching 96%. It outperforms other available solutions
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60 for plasmids recovery from metagenomes and incorporates the thresholding which
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61 allows for exclusion of incertain predictions.
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62 ]]></help>
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63 <citations>
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64 <citation type="doi">10.1093/nar/gkx1321</citation>
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65 </citations>
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66 </tool>
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67