Mercurial > repos > rakesh4osdd > clsi_profile

comparison clsi_profile.xml @ 3:683299422575 draft

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"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
author rakesh4osdd
date Tue, 29 Jun 2021 05:20:41 +0000
parents 62226cd1acb5
children 2a5861818faf
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2:306236ec0511 3:683299422575
19 <option value="clsi_file">CLSI MIC breakpoints</option> 19 <option value="clsi_file">CLSI MIC breakpoints</option>
20 <option value="user_file" >User define MIC breakpoints</option> 20 <option value="user_file" >User define MIC breakpoints</option>
21 </param> 21 </param>
22 <when value="clsi_file"> 22 <when value="clsi_file">
23 <param name="clsi1" type="select" format="csv" label="CSV File"> 23 <param name="clsi1" type="select" format="csv" label="CSV File">
24 <option value="clsi.csv" selected="true">CLSI MIC breakpoints for Bacteria (2020)</option> 24 <option value="test-data/clsi.csv" selected="true">CLSI MIC breakpoints for Bacteria (2020)</option>
25 </param> 25 </param>
26 </when> 26 </when>
27 <when value="user_file"> 27 <when value="user_file">
28 <param name="clsi2" type="data" format="csv" label="CSV File"></param> 28 <param name="clsi2" type="data" format="csv" label="CSV File"></param>
29 </when> 29 </when>
43 <param name="input2" value="clsi.csv"/> 43 <param name="input2" value="clsi.csv"/>
44 <output name="output1" file="output.csv"/> 44 <output name="output1" file="output.csv"/>
45 </test> 45 </test>
46 </tests> 46 </tests>
47 <help><![CDATA[ 47 <help><![CDATA[
48 TODO: Fill in help. 48 Input CSV file example:
49 Strain name,Antibiotics,MIC,unit
50
51 Acinetobacter baumannii A85,Colistin,0.1,mg/L
52
53 Acinetobacter baumannii strain FDA-CDC-AR_0306,polymyxin B,1,mg/L
54
55 Acinetobacter baumannii strain FDA-CDC-AR_0307,polymyxin B,8,mg/L
56
57 Acinetobacter baumannii strain FDA-CDC-AR_0308,polymyxin B,4,mg/L
58
59 Acinetobacter baumannii strain MRSN7834,amoxicillin/clavulanic acid, 16/8,mg/L
60
61 Output CSV file example:
62 Strain name,Colistin,Polymyxin B
63
64 Acinetobacter baumannii A85,Strain could not be classified,NA
65
66 Acinetobacter baumannii strain FDA-CDC-AR_0306,NA,Strain could not be classified
67
68 Acinetobacter baumannii strain FDA-CDC-AR_0307,NA,Resistant
69
70 Acinetobacter baumannii strain FDA-CDC-AR_0308,NA,Resistant
49 ]]></help> 71 ]]></help>
72 <citations>
73 <citation type="bibtex">@ARTICLE{Sharma_2021,
74 author = {Tina Sharma and Rakesh Kumar and Anshu Bhardwaj},
75 title = {ASIST: Antimicrobial Susceptibility standards based phenotypes},
76 journal = {},
77 year = {2021},
78 volume = {},
79 pages = {},
80 url = {https://ab-openlab.csir.res.in/asist}
81 }
82 </citation>
83 </citations>
50 </tool> 84 </tool>