Mercurial > repos > nml > spatyper
view spatyper.xml @ 0:52d69f74b19e draft
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e
author | nml |
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date | Mon, 20 Mar 2023 20:16:56 +0000 |
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children | 2c353e0dacae |
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<tool id="spatyper" name="Generate spa type identification" version="@VERSION@+galaxy0" profile="21.01"> <macros> <token name="@VERSION@">0.3.3</token> </macros> <requirements> <requirement type="package" version="@VERSION@">spatyper</requirement> </requirements> <command detect_errors="aggressive"> <![CDATA[ spaTyper -f '${input1}' -r '${input2}' > '${output1}' ]]> </command> <inputs> <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."/> <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)"/> </inputs> <outputs> <data name="output1" format="txt" /> </outputs> <tests> <test> <param name="input1" value="input.fasta"/> <param name="input2" value="sparepeats.fasta"/> <output name="output1"> <assert_contents> <has_text text = "t11215" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ :: USAGE: spaTyper [-h] [-r REPEAT_FILE] [-o REPEAT_ORDER_FILE] [-d FOLDER] [-f FASTA [FASTA ...]] [-g GLOB] [-e] [--output OUTPUT] [--version] [--debug] [--info] spaTyper.py: Get spa types Version: 0.3.3 License: GPLv3 Prints spa type to stdout It will download sparepeats.fasta and spatypes.txt to repository directory if files not provided or already in directory. It can be loaded as a python module. Python 3 version only. Options: -h show this help message and exit -r REPEAT_FILE (http://spa.ridom.de/dynamic/sparepeats.fasta) -o REPEAT_ORDER_FILE (http://spa.ridom.de/dynamic/spatypes.txt) -d Folder to save downloaded files from Ridom/Spa server -f List of one or more fasta files. -g Uses unix style pathname expansion to run spa typing on all files. If your shell autoexpands wildcards use -f. -e Do PCR product enrichment. [Default: False] ]]></help> <citations> <citation type="bibtex"> @misc{githubseqtk, author = {HCGB}, year = {2020}, title = {spaTyper}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://github.com/HCGB-IGTP/spaTyper}, }</citation> </citations> </tool>