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annotate asist.xml @ 0:c1a77856070c draft

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