annotate clsi_profile.xml @ 11:7dcc0e93288b draft default tip

"planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f590c3b1d71a9b8f2030909fa488b4ac0c3caed8-dirty"
author rakesh4osdd
date Wed, 30 Jun 2021 07:13:29 +0000
parents 2a5861818faf
children
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2a5861818faf "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit 7169e85ac6d230af9309b0deacecd4dc61e0a915"
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1 <tool id="clsi_profile" name="CLSI Profile" version="0.1.7" python_template_version="3.5">
0
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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
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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>
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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="test-data/clsi.csv" selected="true">CLSI MIC breakpoints for Bacteria (2020)</option>
0
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25 </param>
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26 </when>
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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>
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30 </conditional>
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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>
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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>
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38 <data name="output1" format="csv" />
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="input1" value="input.csv"/>
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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>
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46 </tests>
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47 <help><![CDATA[
3
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48 Input CSV file example:
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
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49 Strain name,Antibiotics,MIC,unit
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50
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
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51 Acinetobacter baumannii A85,Colistin,0.1,mg/L
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52
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
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53 Acinetobacter baumannii strain FDA-CDC-AR_0306,polymyxin B,1,mg/L
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54
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
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55 Acinetobacter baumannii strain FDA-CDC-AR_0307,polymyxin B,8,mg/L
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56
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
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57 Acinetobacter baumannii strain FDA-CDC-AR_0308,polymyxin B,4,mg/L
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58
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
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59 Acinetobacter baumannii strain MRSN7834,amoxicillin/clavulanic acid, 16/8,mg/L
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60
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
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61 Output CSV file example:
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62 Strain name,Colistin,Polymyxin B
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63
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
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64 Acinetobacter baumannii A85,Strain could not be classified,NA
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65
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
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66 Acinetobacter baumannii strain FDA-CDC-AR_0306,NA,Strain could not be classified
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67
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
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68 Acinetobacter baumannii strain FDA-CDC-AR_0307,NA,Resistant
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69
683299422575 "planemo upload for repository https://github.com/rakesh4osdd/asist/tree/master commit f085b88bf75f7b45ac3b0c4e1c39214c0ac0b67d"
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70 Acinetobacter baumannii strain FDA-CDC-AR_0308,NA,Resistant
0
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71 ]]></help>
3
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72 <citations>
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73 <citation type="bibtex">@ARTICLE{Sharma_2021,
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74 author = {Tina Sharma and Rakesh Kumar and Anshu Bhardwaj},
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75 title = {ASIST: Antimicrobial Susceptibility standards based phenotypes},
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76 journal = {},
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77 year = {2021},
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78 volume = {},
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79 pages = {},
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80 url = {https://ab-openlab.csir.res.in/asist}
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81 }
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82 </citation>
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83 </citations>
0
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84 </tool>