Mercurial > repos > rakesh4osdd > clsi_profile

annotate clsi_profile.xml @ 2:306236ec0511 draft

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author rakesh4osdd
date Fri, 11 Jun 2021 13:20:08 +0000
parents 62226cd1acb5
children 683299422575
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62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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1 <tool id="clsi_profile" name="CLSI Profile" version="0.1.6" 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>
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3 <requirements>
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4 <requirement type="package">pandas</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 #if $input2.type_selector == "clsi_file"
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8 python "${__tool_directory__}/clsi_profile.py" "$input1" "${__tool_directory__}/$input2.clsi1" "$output1"
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9 #else
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10 python "${__tool_directory__}/clsi_profile.py" "$input1" "$input2.clsi2" "$output1"
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11 #end if
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12 ]]></command>
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13 <inputs>
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14
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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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>
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16
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17 <conditional name="input2">
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18 <param name="type_selector" type="select" label="Choose MIC Breakpoints">
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19 <option value="clsi_file">CLSI MIC breakpoints</option>
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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"
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21 </param>
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22 <when value="clsi_file">
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23 <param name="clsi1" type="select" format="csv" label="CSV File">
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24 <option value="clsi.csv" selected="true">CLSI MIC breakpoints for Bacteria (2020)</option>
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25 </param>
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26 </when>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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27 <when value="user_file">
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28 <param name="clsi2" type="data" format="csv" label="CSV File"></param>
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29 </when>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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30 </conditional>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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31
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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32 </inputs>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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33 <!--inputs>
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34 <param type="data" name="input1" format="csv" />
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35 <param type="data" name="input2" format="csv" />
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36 </inputs-->
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37 <outputs>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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38 <data name="output1" format="csv" />
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39 </outputs>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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40 <tests>
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41 <test>
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42 <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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43 <param name="input2" value="clsi.csv"/>
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44 <output name="output1" file="output.csv"/>
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45 </test>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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46 </tests>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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47 <help><![CDATA[
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48 TODO: Fill in help.
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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49 ]]></help>
62226cd1acb5 "planemo upload for repository https://github.com/rakesh4osdd/clsi_profile/tree/master commit ae6f2bc197b28000c56f6368ad044b350bc34f6a"
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50 </tool>