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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit f3fb3601f726fd8f18dc42e6a83a9f92a7f27712
author nml
date Tue, 18 Apr 2023 23:06:33 +0000
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0d2243ed7833 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit f3fb3601f726fd8f18dc42e6a83a9f92a7f27712
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1 <tool id="spatyper" name="Generate spa type identification" version="@VERSION@+galaxy1" profile="20.01">
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2 <macros>
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3 <token name="@VERSION@">0.3.3</token>
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4 </macros>
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5 <requirements>
4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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6 <requirement type="package" version="@VERSION@">spatyper</requirement>
4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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7 </requirements>
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8 <command detect_errors="aggressive"> <![CDATA[
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0d2243ed7833 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit f3fb3601f726fd8f18dc42e6a83a9f92a7f27712
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9 spaTyper -f '${input}' --output '${output}'
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10 ]]> </command>
4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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11 <inputs>
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0d2243ed7833 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit f3fb3601f726fd8f18dc42e6a83a9f92a7f27712
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12 <param type="data" name="input" format="fasta" label="SPA Fasta file" help="Staphylococcus aureus - staphylococcal protein A fasta file. This will be assigned a type based on its repeat region."/>
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4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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13 </inputs>
4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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14 <outputs>
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15 <data name="output" format="tsv"/>
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16 </outputs>
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17 <tests>
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18 <test>
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0d2243ed7833 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit f3fb3601f726fd8f18dc42e6a83a9f92a7f27712
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19 <param name="input" value="input.fasta"/>
0d2243ed7833 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit f3fb3601f726fd8f18dc42e6a83a9f92a7f27712
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20 <output name="output" file="output.tsv" ftype="tsv"/>
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4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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21 </test>
4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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22 </tests>
4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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23 <help><![CDATA[
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24 ::
4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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25
4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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26 USAGE: spaTyper [-h] [-r REPEAT_FILE] [-o REPEAT_ORDER_FILE] [-d FOLDER] [-f FASTA [FASTA ...]] [-g GLOB] [-e] [--output OUTPUT] [--version] [--debug] [--info]
4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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28 spaTyper.py: Get spa types
4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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30 Version: 0.3.3
4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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31 License: GPLv3
4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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32 Prints spa type to stdout
4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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33
4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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34 It will download sparepeats.fasta and spatypes.txt to repository directory
4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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35 if files not provided or already in directory. It can be loaded as a python
4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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36 module. Python 3 version only.
4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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37
4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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38 Options: -h show this help message and exit
4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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39 -r REPEAT_FILE (http://spa.ridom.de/dynamic/sparepeats.fasta)
4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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40 -o REPEAT_ORDER_FILE (http://spa.ridom.de/dynamic/spatypes.txt)
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41 -d Folder to save downloaded files from Ridom/Spa server
4ee5c28a3d1b planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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42 -f List of one or more fasta files.
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43 -g Uses unix style pathname expansion to run spa typing on all files. If your shell autoexpands wildcards use -f.
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44 -e Do PCR product enrichment. [Default: False]
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45
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46 ]]></help>
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47 <citations>
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48 <citation type="bibtex">
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49 @misc{githubseqtk,
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50 author = {HCGB},
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51 year = {2020},
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52 title = {spaTyper},
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53 publisher = {GitHub},
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54 journal = {GitHub repository},
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55 url = {https://github.com/HCGB-IGTP/spaTyper},
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56 }</citation>
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57 </citations>
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58 </tool>