Mercurial > repos > rakesh4osdd > asist
comparison asist.xml @ 0:c1a77856070c draft
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
| author | rakesh4osdd |
|---|---|
| date | Sat, 26 Jun 2021 07:27:53 +0000 |
| parents | |
| children | 6a0a21d3fcea |
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| -1:000000000000 | 0:c1a77856070c |
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| 1 <tool id="asist" name="ASIST" version="1.0.1" python_template_version="3.5"> | |
| 2 <description>Antimicrobial Susceptibility standards based phenotypes</description> | |
| 3 <requirements> | |
| 4 <requirement type="package">pandas</requirement> | |
| 5 </requirements> | |
| 6 <version_command>python -c "import pandas; print(pandas.__version__)"</version_command> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 "${__tool_directory__}/asist_dynamic.py" "$input1" "$output1" | |
| 9 ]]></command> | |
| 10 <inputs> | |
| 11 <param type="data" name="input1" format="csv" /> | |
| 12 </inputs> | |
| 13 <outputs> | |
| 14 <data name="output1" format="csv" from_work_dir="test-data/asist_output.csv" /> | |
| 15 </outputs> | |
| 16 <tests> | |
| 17 <test> | |
| 18 <param name="input1" value="test-data/asist_input.csv"/> | |
| 19 <output name="output1" file="test-data/asist_output.csv"/> | |
| 20 </test> | |
| 21 </tests> | |
| 22 <help><![CDATA[ | |
| 23 Input CSV file example: | |
| 24 Strain name,Amikacin,Tobramycin,Gentamycin,Imipenem | |
| 25 Strain name,Aminoglycoside,Aminoglycoside,Aminoglycoside,Beta-lactams-Carbapenems | |
| 26 Acinetobacter baumannii strain FDA-CDC-AR_0288,Resistant,Resistant,Resistant,Resistant | |
| 27 Acinetobacter baumannii strain FDA-CDC-AR_0303,Resistant,Resistant,Resistant,Resistant | |
| 28 Acinetobacter baumannii strain FDA-CDC-AR_0304,NA,Resistant,Resistant,Resistant | |
| 29 Output CSV file example: | |
| 30 Strain name,Strain phenotype,Amikacin,Tobramycin,Gentamycin,Imipenem | |
| 31 Strain name,Strain could not be classified,Aminoglycoside,Aminoglycoside,Aminoglycoside,Beta-lactams-Carbapenems | |
| 32 Acinetobacter baumannii strain FDA-CDC-AR_0288,Strain could not be classified,Resistant,Resistant,Resistant,Resistant | |
| 33 Acinetobacter baumannii strain FDA-CDC-AR_0303,Strain could not be classified,Resistant,Resistant,Resistant,Resistant | |
| 34 Acinetobacter baumannii strain FDA-CDC-AR_0304,Strain could not be classified,NA,Resistant,Resistant,Resistant | |
| 35 ]]></help> | |
| 36 <citations> | |
| 37 <citation type="bibtex">@ARTICLE{Sharma_2021, | |
| 38 author = {Tina Sharma and Rakesh Kumar and Anshu Bhardwaj}, | |
| 39 title = {ASIST: Antimicrobial Susceptibility standards based phenotypes}, | |
| 40 journal = {}, | |
| 41 year = {2021}, | |
| 42 volume = {}, | |
| 43 pages = {}, | |
| 44 url = {https://ab-openlab.csir.res.in/asist} | |
| 45 } | |
| 46 </citation> | |
| 47 </citations> | |
| 48 </tool> |