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annotate spatyper.xml @ 0:52d69f74b19e draft

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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
author nml
date Mon, 20 Mar 2023 20:16:56 +0000
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52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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1 <tool id="spatyper" name="Generate spa type identification" version="@VERSION@+galaxy0" profile="21.01">
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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>
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6 <requirement type="package" version="@VERSION@">spatyper</requirement>
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7 </requirements>
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8 <command detect_errors="aggressive"> <![CDATA[
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9 spaTyper -f '${input1}' -r '${input2}' > '${output1}'
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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10 ]]> </command>
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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11 <inputs>
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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12 <param type="data" name="input1" 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."/>
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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13 <param type="data" name="input2" format="fasta" label="Repeats Library Multifasta" help="A multifasta representing a set of known repeat regions found in staphylococcal protein A. This can be downloaded at (http://spa.ridom.de/dynamic/sparepeats.fasta)"/>
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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14 </inputs>
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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15 <outputs>
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16 <data name="output1" format="txt" />
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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17 </outputs>
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18 <tests>
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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19 <test>
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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20 <param name="input1" value="input.fasta"/>
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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21 <param name="input2" value="sparepeats.fasta"/>
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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22 <output name="output1">
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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23 <assert_contents>
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24 <has_text text = "t11215" />
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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25 </assert_contents>
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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26 </output>
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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27 </test>
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28 </tests>
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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29 <help><![CDATA[
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30 ::
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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31
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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32 USAGE: spaTyper [-h] [-r REPEAT_FILE] [-o REPEAT_ORDER_FILE] [-d FOLDER] [-f FASTA [FASTA ...]] [-g GLOB] [-e] [--output OUTPUT] [--version] [--debug] [--info]
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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33
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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34 spaTyper.py: Get spa types
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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35
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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36 Version: 0.3.3
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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37 License: GPLv3
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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38 Prints spa type to stdout
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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39
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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40 It will download sparepeats.fasta and spatypes.txt to repository directory
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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41 if files not provided or already in directory. It can be loaded as a python
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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42 module. Python 3 version only.
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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43
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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44 Options: -h show this help message and exit
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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45 -r REPEAT_FILE (http://spa.ridom.de/dynamic/sparepeats.fasta)
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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46 -o REPEAT_ORDER_FILE (http://spa.ridom.de/dynamic/spatypes.txt)
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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47 -d Folder to save downloaded files from Ridom/Spa server
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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48 -f List of one or more fasta files.
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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49 -g Uses unix style pathname expansion to run spa typing on all files. If your shell autoexpands wildcards use -f.
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50 -e Do PCR product enrichment. [Default: False]
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51
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52 ]]></help>
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53 <citations>
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54 <citation type="bibtex">
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55 @misc{githubseqtk,
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56 author = {HCGB},
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57 year = {2020},
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58 title = {spaTyper},
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59 publisher = {GitHub},
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60 journal = {GitHub repository},
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61 url = {https://github.com/HCGB-IGTP/spaTyper},
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62 }</citation>
52d69f74b19e planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
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63 </citations>
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64 </tool>