Mercurial > repos > ecology > vigiechiro_idcorrect_2ndlayer

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
author ecology
date Wed, 13 Mar 2019 11:18:36 -0400
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6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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1 <tool id="vigiechiro_idcorrect_2ndlayer" name="Tadarida data cleaner" version="@VERSION@">
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2 <description>clean data from animal detection on acoustic recordings</description>
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3 <macros>
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4 <import>vigiechiro_macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="1.10.4">r-data.table</requirement>
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8 <requirement type="package" version="4.6_12">r-randomforest</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 Rscript
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12 '$__tool_directory__/IdCorrect_2ndLayer.R' '$participation_file'
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13
6681b6ba1d7e planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
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14 #if $learner.condi_learner == "custom"
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15 '$learner.user_learner'
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16 #else
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17 '$__tool_directory__/ClassifEspC2b_180222.learner'
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18 #end if
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19 '${participation_file.name}'
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20 '$output'
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21 ]]>
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22 </command>
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23 <inputs>
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24 <param name="participation_file" type="data" format="csv" label="Participation file" help="Summary table of TadaridaC"/>
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25 <param name="learner" type="data" label="Choose your leaner" format="rdata"/>
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26 <conditional name="learner">
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27 <param name="condi_learner" type="select" label="Select a classifier" help="Default is ClassifEspC2b_180222">
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28 <option value="c18">ClassifEspC2b_180222</option>
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29 <option value="custom">Custom Classifier</option>
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30 </param>
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31 <when value="c18">
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32 </when>
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33 <when value="custom">
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34 <param name="user_learner" type="data" label="Choose your classifier" format="rdata"/>
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35 </when>
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36 </conditional>
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37 </inputs>
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38 <outputs>
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39 <data name="output" from_work_dir="output.tabular" format="tabular"/>
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="participation_file" value="IdCor2Layer_Test1_obs.csv"/>
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44 <param name="condi_learner" value="default_learner"/>
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45 <output name="output" file="IdCor2Layer_Test1_out.tabular"/>
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46 </test>
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47 </tests>
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48 <help><![CDATA[
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49
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50 .. class:: infomark
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51
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52 ==========================
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53 Tadarida data cleaner
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54 ==========================
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55
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56 **What it does**
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57
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58 This tool intends to correct ids from 1st layer of Tadarida software, and improves data output according to context (= the whole output of a sampling session).
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59
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60 **Arguments**
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61
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62 It should be called with 2 consecutive arguments :
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63
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64 - a summary table of TadaridaC output from vigiechiro.herokuapp.com web portal.
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65 - the 2nd layer classifier built on validated id in Vigie-Chiro database (eg : "ClassifEspC2b_180222.learner")
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66 ]]></help>
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67 <expand macro="vigiechiro_bibref" />
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68 </tool>