Mercurial > repos > rakesh4osdd > asist
annotate README.rst @ 7:fb83dfff5679 draft
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author | rakesh4osdd |
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date | Wed, 30 Jun 2021 05:57:47 +0000 |
parents | 734777d3c253 |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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1 # clsi_profile |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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3 CLSI profile for ASIST using the CLSI standards 2020 by AST profiling for bacteria. It help to generate the input file for ASIST program based on MIC values provided by CLSI based AST profiling. |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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3 | 5 # ASIST: Antimicrobial Susceptibility standards |
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6 |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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7 In the first column strain names will be mentioned, the second column will be left blank for getting resistance phenotype, starting two rows will comprise antibiotic names (first row) and antibiotic classes (second row). The data for the resistance profile will then start from the C3 column of an excel file which can be converted into a .csv file. Since B3 is left blank, after implementing the algorithm, column B3 will be filled with the resistance phenotype (susceptible, MDR, XDR, PDR). |
c1a77856070c
"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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9 **Example Input CSV file:** |
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11 Strain name,Resistance_phenotype,Antibiotic_A1,Antibiotic_A2,Antibiotic_A_N |
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12 Strain_1,Phenotype_1,Resistant,Resistant,Resistant |
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13 Strain_2,Phenotype_2,Resistant,Susceptible,Resistant |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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3 | 15 Link to the code : https://github.com/rakesh4osdd/clsi_profile , https://github.com/rakesh4osdd/asist |
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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f5b374bef15145c893ffdd3a7d2f2978d8052184-dirty"
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18 # ASIST tool suite |
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20 These tools can be install from Galaxy toolshed to a Galaxy installation https://galaxyproject.org/admin/get-galaxy/. |