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clsi_profile.xml
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<tool id="clsi_profile" name="ASIST_CLSI_Breakpoint" version="0.1.8">
<description>CLSI MIC breakpoints profile</description>
<!--command interpreter="python">clsi_profile.py "$input" "$clsi" "$output"</command-->
<command detect_errors="exit_code">
<![CDATA[
#if $input2.type_selector == "eucast_file"
python "${__tool_directory__}/eucast_profile.py" "$input" "$input2.clsi" "$output"
#else
python "${__tool_directory__}/clsi_profile.py" "$input" "$input2.clsi" "$output"
#end if
]]>
</command>
<inputs>
<param name="input" type="data" format="csv" label="Input file of Antimicrobial Susceptibility Testing (AST) MIC values for strains" help="Input AST file in CSV format (Please see example given below)"></param>
<conditional name="input2">
<param name="type_selector" type="select" label="Choose MIC Breakpoints">
<option value="clsi_file">CLSI MIC breakpoints</option>
<option value="eucast_file" >EUCAST MIC breakpoints</option>
<option value="user_file" >User define MIC breakpoints</option>
</param>
<when value="clsi_file">
<param name="clsi" type="select" format="csv" label="CSV File">
<option value="/sandisk/ab-openlab/asist_galaxy/galaxy/tools/asist/CLSI/CLSI-2022.csv" selected="true">CLSI MIC breakpoints for Bacteria (2022)</option>
</param>
</when>
<when value="eucast_file">
<param name="clsi" type="select" format="csv" label="CSV File">
<option value="/sandisk/ab-openlab/asist_galaxy/galaxy/tools/asist/CLSI/EUCAST-2022.csv">EUCAST MIC breakpoints for Bacteria (2022)</option>
</param>
</when>
<when value="user_file">
<param name="clsi" type="data" format="csv" label="CSV File"></param>
</when>
</conditional>
</inputs>
<outputs>
<data name="output" format="csv"/>
</outputs>
<help>
.. class:: infomark
**USAGE:** Please provide the input CSV file containing AST MIC values for the tested strains.
**Input AST file example:** ::
Strain name,Antibiotics,MIC,Unit
Acinetobacter baumannii A85,Colistin,0.1,mg/L
Acinetobacter baumannii AB307-0294,Imipenem,1,mg/L
Acinetobacter baumannii AB307-0294,Ampicillin,0,mg/L
Acinetobacter baumannii ORAB01,piperacillin/tazobactam,>64/4,mg/L
Acinetobacter baumannii strain MRSN7100,amoxicillin/clavulanic acid, 16/8,mg/L
Acinetobacter baumannii AB307-0294,piperacillin/tazobactam,0,mg/L
Acinetobacter baumannii DU202,Ampicillin/sulbactam,>=0.3,mg/L
------------------------------------------------------------------------------------
Note: Antibiotics must not have more than one MIC value for same Strain name. All MIC
units must be same as MIC breakpoints. eg. mg/L.
**Input CLSI MIC breakpoints file example:** ::
Antibiotics,Susceptible,Resistant, Intermediate
Colistin,-,≥ 4,2
Imipenem,≤ 2,≥ 8,4
Ciprofloxacin,≤ 1,≥ 4,2
Piperacillin/ tazobactam,≤ 16/4,≥ 128/4,32/4-64/4
Ticarcillin/ clavulanic acid,≤ 16/2,≥ 128/2,32/2-64/2
------------------------------------------------------------------------------------
Note: All MIC units must be same. eg. mg/L.
**Output example:** ::
Strain name,Resistance_phenotype,Imipenem,Piperacillin/tazobactam,Colistin
Acinetobacter baumannii A85,,NA,NA,Susceptible
Acinetobacter baumannii AB307-0294,,Susceptible,Strain could not be classified,NA
Acinetobacter baumannii ORAB01,,NA,Intermediate,NA
------------------------------------------------------------------------------------
Note: Only CLSI MIC breakpoints based antibiotics are present in the output.
'NA' :- Antibiotic is 'Not Available'
** Default MIC sign for comparing Susceptible breakpoints with measurement value is "≤"**
** Default MIC sign for comparing Resistant breakpoints with measurement value is "≥"**
</help>
</tool>