Mercurial > repos > ecology > vigiechiro_idcorrect_2ndlayer

comparison IdCorrect_2ndLayer_en.xml @ 0:6681b6ba1d7e draft

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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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-1:000000000000 0:6681b6ba1d7e
1 <tool id="vigiechiro_idcorrect_2ndlayer" name="Tadarida data cleaner" version="@VERSION@">
2 <description>clean data from animal detection on acoustic recordings</description>
3 <macros>
4 <import>vigiechiro_macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="1.10.4">r-data.table</requirement>
8 <requirement type="package" version="4.6_12">r-randomforest</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 Rscript
12 '$__tool_directory__/IdCorrect_2ndLayer.R' '$participation_file'
13
14 #if $learner.condi_learner == "custom"
15 '$learner.user_learner'
16 #else
17 '$__tool_directory__/ClassifEspC2b_180222.learner'
18 #end if
19 '${participation_file.name}'
20 '$output'
21 ]]>
22 </command>
23 <inputs>
24 <param name="participation_file" type="data" format="csv" label="Participation file" help="Summary table of TadaridaC"/>
25 <param name="learner" type="data" label="Choose your leaner" format="rdata"/>
26 <conditional name="learner">
27 <param name="condi_learner" type="select" label="Select a classifier" help="Default is ClassifEspC2b_180222">
28 <option value="c18">ClassifEspC2b_180222</option>
29 <option value="custom">Custom Classifier</option>
30 </param>
31 <when value="c18">
32 </when>
33 <when value="custom">
34 <param name="user_learner" type="data" label="Choose your classifier" format="rdata"/>
35 </when>
36 </conditional>
37 </inputs>
38 <outputs>
39 <data name="output" from_work_dir="output.tabular" format="tabular"/>
40 </outputs>
41 <tests>
42 <test>
43 <param name="participation_file" value="IdCor2Layer_Test1_obs.csv"/>
44 <param name="condi_learner" value="default_learner"/>
45 <output name="output" file="IdCor2Layer_Test1_out.tabular"/>
46 </test>
47 </tests>
48 <help><![CDATA[
49
50 .. class:: infomark
51
52 ==========================
53 Tadarida data cleaner
54 ==========================
55
56 **What it does**
57
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).
59
60 **Arguments**
61
62 It should be called with 2 consecutive arguments :
63
64 - a summary table of TadaridaC output from vigiechiro.herokuapp.com web portal.
65 - the 2nd layer classifier built on validated id in Vigie-Chiro database (eg : "ClassifEspC2b_180222.learner")
66 ]]></help>
67 <expand macro="vigiechiro_bibref" />
68 </tool>