Mercurial > repos > rakesh4osdd > asist
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/asist.xml Sat Jun 26 07:27:53 2021 +0000 @@ -0,0 +1,48 @@ +<tool id="asist" name="ASIST" version="1.0.1" python_template_version="3.5"> + <description>Antimicrobial Susceptibility standards based phenotypes</description> + <requirements> + <requirement type="package">pandas</requirement> + </requirements> + <version_command>python -c "import pandas; print(pandas.__version__)"</version_command> + <command detect_errors="exit_code"><![CDATA[ + "${__tool_directory__}/asist_dynamic.py" "$input1" "$output1" + ]]></command> + <inputs> + <param type="data" name="input1" format="csv" /> + </inputs> + <outputs> + <data name="output1" format="csv" from_work_dir="test-data/asist_output.csv" /> + </outputs> + <tests> + <test> + <param name="input1" value="test-data/asist_input.csv"/> + <output name="output1" file="test-data/asist_output.csv"/> + </test> + </tests> + <help><![CDATA[ + Input CSV file example: + Strain name,Amikacin,Tobramycin,Gentamycin,Imipenem + Strain name,Aminoglycoside,Aminoglycoside,Aminoglycoside,Beta-lactams-Carbapenems + Acinetobacter baumannii strain FDA-CDC-AR_0288,Resistant,Resistant,Resistant,Resistant + Acinetobacter baumannii strain FDA-CDC-AR_0303,Resistant,Resistant,Resistant,Resistant + Acinetobacter baumannii strain FDA-CDC-AR_0304,NA,Resistant,Resistant,Resistant + Output CSV file example: + Strain name,Strain phenotype,Amikacin,Tobramycin,Gentamycin,Imipenem + Strain name,Strain could not be classified,Aminoglycoside,Aminoglycoside,Aminoglycoside,Beta-lactams-Carbapenems + Acinetobacter baumannii strain FDA-CDC-AR_0288,Strain could not be classified,Resistant,Resistant,Resistant,Resistant + Acinetobacter baumannii strain FDA-CDC-AR_0303,Strain could not be classified,Resistant,Resistant,Resistant,Resistant + Acinetobacter baumannii strain FDA-CDC-AR_0304,Strain could not be classified,NA,Resistant,Resistant,Resistant + ]]></help> + <citations> + <citation type="bibtex">@ARTICLE{Sharma_2021, + author = {Tina Sharma and Rakesh Kumar and Anshu Bhardwaj}, + title = {ASIST: Antimicrobial Susceptibility standards based phenotypes}, + journal = {}, + year = {2021}, + volume = {}, + pages = {}, + url = {https://ab-openlab.csir.res.in/asist} + } + </citation> + </citations> +</tool>