Mercurial > repos > rakesh4osdd > clsi_profile

annotate dump/clsi_profile.xml @ 0:62226cd1acb5 draft

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"planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
author rakesh4osdd
date Fri, 11 Jun 2021 12:36:25 +0000
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62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
rakesh4osdd
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1 <tool id="clsi_profile" name="CLSI Profile" version="0.1.0" python_template_version="3.5">
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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2 <description>MIC profile using CLSI MIC breakpoints</description>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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3
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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4 <command detect_errors="exit_code"><![CDATA[
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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5 python '$__tool_directory__/clsi_profile.py' '$input1' '$input2' '$output1'
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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6 ]]></command>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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7 <inputs>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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8 <param type="data" name="input1" format="csv" />
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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9 <param type="data" name="input2" format="csv" />
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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10 </inputs>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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11 <outputs>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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12 <data name="output1" format="csv" />
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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13 </outputs>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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14 <tests>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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15 <test>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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16 <param name="input1" value="input.csv"/>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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17 <param name="input2" value="clsi.csv"/>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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18 <output name="output1" file="output.csv"/>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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19 </test>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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20 </tests>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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21 <help><![CDATA[
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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22 Examples Files:
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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23 **CLSI MIC breakpoint file example:** ::
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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24
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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25 Antibiotics,Susceptible,Resistant,Intermediate
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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26 Amikacin,≤ 16,≥ 64,32
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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27 Tobramycin,≤ 4,≥ 16,8
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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28 Gentamicin,≤ 4,≥ 16,8
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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29
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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30 **AST MIC value file example:** ::
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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31 Strain name,Antibiotics,MIC
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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32 Strain1,Amikacin,≤ 16
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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33 Strain2,Tobramycin,≤ 4
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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34 Strain3,Gentamicin,≤ 4
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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35 ]]></help>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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36 </tool>