annotate clsi_profile.xml @ 5:3c27e5c2a8e9 draft

"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit d4b81c15919b4b87d215eaf1b792c8f251665647"
author rakesh4osdd
date Tue, 29 Jun 2021 12:58:49 +0000
parents 2a5861818faf
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
2a5861818faf "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
rakesh4osdd
parents: 3
diff changeset
1 <tool id="clsi_profile" name="CLSI Profile" version="0.1.7" python_template_version="3.5">
0
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
2 <description>MIC profile using CLSI MIC breakpoints</description>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
3 <requirements>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
4 <requirement type="package">pandas</requirement>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
5 </requirements>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
6 <command detect_errors="exit_code"><![CDATA[
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
7 #if $input2.type_selector == "clsi_file"
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
8 python "${__tool_directory__}/clsi_profile.py" "$input1" "${__tool_directory__}/$input2.clsi1" "$output1"
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
9 #else
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
10 python "${__tool_directory__}/clsi_profile.py" "$input1" "$input2.clsi2" "$output1"
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
11 #end if
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
12 ]]></command>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
13 <inputs>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
14
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
15 <param name="input1" 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>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
16
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
17 <conditional name="input2">
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
18 <param name="type_selector" type="select" label="Choose MIC Breakpoints">
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
19 <option value="clsi_file">CLSI MIC breakpoints</option>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
20 <option value="user_file" >User define MIC breakpoints</option>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
21 </param>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
22 <when value="clsi_file">
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
23 <param name="clsi1" type="select" format="csv" label="CSV File">
3
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
24 <option value="test-data/clsi.csv" selected="true">CLSI MIC breakpoints for Bacteria (2020)</option>
0
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
25 </param>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
26 </when>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
27 <when value="user_file">
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
28 <param name="clsi2" type="data" format="csv" label="CSV File"></param>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
29 </when>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
30 </conditional>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
31
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
32 </inputs>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
33 <!--inputs>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
34 <param type="data" name="input1" format="csv" />
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
35 <param type="data" name="input2" format="csv" />
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
36 </inputs-->
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
37 <outputs>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
38 <data name="output1" format="csv" />
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
39 </outputs>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
40 <tests>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
41 <test>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
42 <param name="input1" value="input.csv"/>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
43 <param name="input2" value="clsi.csv"/>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
44 <output name="output1" file="output.csv"/>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
45 </test>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
46 </tests>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
47 <help><![CDATA[
3
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
48 Input CSV file example:
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
49 Strain name,Antibiotics,MIC,unit
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
50
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
51 Acinetobacter baumannii A85,Colistin,0.1,mg/L
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
52
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
53 Acinetobacter baumannii strain FDA-CDC-AR_0306,polymyxin B,1,mg/L
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
54
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
55 Acinetobacter baumannii strain FDA-CDC-AR_0307,polymyxin B,8,mg/L
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
56
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
57 Acinetobacter baumannii strain FDA-CDC-AR_0308,polymyxin B,4,mg/L
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
58
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
59 Acinetobacter baumannii strain MRSN7834,amoxicillin/clavulanic acid, 16/8,mg/L
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
60
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
61 Output CSV file example:
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
62 Strain name,Colistin,Polymyxin B
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
63
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
64 Acinetobacter baumannii A85,Strain could not be classified,NA
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
65
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
66 Acinetobacter baumannii strain FDA-CDC-AR_0306,NA,Strain could not be classified
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
67
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
68 Acinetobacter baumannii strain FDA-CDC-AR_0307,NA,Resistant
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
69
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
70 Acinetobacter baumannii strain FDA-CDC-AR_0308,NA,Resistant
0
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
71 ]]></help>
3
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
72 <citations>
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
73 <citation type="bibtex">@ARTICLE{Sharma_2021,
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
74 author = {Tina Sharma and Rakesh Kumar and Anshu Bhardwaj},
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
75 title = {ASIST: Antimicrobial Susceptibility standards based phenotypes},
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
76 journal = {},
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
77 year = {2021},
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
78 volume = {},
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
79 pages = {},
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
80 url = {https://ab-openlab.csir.res.in/asist}
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
81 }
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
82 </citation>
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
rakesh4osdd
parents: 0
diff changeset
83 </citations>
0
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
parents:
diff changeset
84 </tool>