Mercurial > repos > ecology > vigiechiro_bilanenrichirp
comparison BilanEnrichiRPen.xml @ 0:c55e09a8b4c8 draft
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
author | ecology |
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date | Wed, 13 Mar 2019 11:17:44 -0400 |
parents | |
children | be4e28da3919 |
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-1:000000000000 | 0:c55e09a8b4c8 |
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1 <tool id="vigiechiro_bilanenrichirp" name="Advanced restitution: 'Routier'or 'Pedestre' protocols" version="@VERSION@"> | |
2 <description>from Animal Detection on Acoustic Recordings</description> | |
3 <macros> | |
4 <import>vigiechiro_macros.xml</import> | |
5 </macros> | |
6 <expand macro="vigiechiro_bilanPF_bilanRP_requirements"/> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 Rscript '$__tool_directory__/BilanEnrichiRP.R' | |
9 '$idc2' | |
10 '$__tool_directory__/refRPSeuil50.csv' | |
11 '$__tool_directory__/SpeciesList.csv' | |
12 && | |
13 tail -n +2 output-summaryRP.html > tmp && mv tmp output-summaryRP.html && | |
14 tail -n +2 output-detailRP.html > tmp && mv tmp output-detailRP.html | |
15 ]]> | |
16 </command> | |
17 <inputs> | |
18 <param name="idc2" type="data" format="tabular" label="Corrected and validated observation file" help="Use output file from 'Tadarida identifications integration' : a sampling session file corrected and validated. Routier or Pedestre protocol"/> | |
19 <param name="output_choice" type="select" label="Select a summarised or detailed display" multiple="true" optional="false" help="Chose whether your want a summarised or detailed display"> | |
20 <option value="detailed" selected="true">detailed output</option> | |
21 <option value="summarised">summarised output</option> | |
22 </param> | |
23 </inputs> | |
24 <outputs> | |
25 <data name="output_summary_tabular" format="tabular" from_work_dir="output-summaryRP.tabular" label="${tool.name} on ${on_string} Summary table"> | |
26 <filter>'summarised' in output_choice</filter> | |
27 </data> | |
28 <data name="output_summary_html" format="html" from_work_dir="output-summaryRP.html" label="${tool.name} on ${on_string} Summary html"> | |
29 <filter>'summarised' in output_choice</filter> | |
30 </data> | |
31 <data name="output_detail_tabular" format="tabular" from_work_dir="output-detailRP.tabular" label="${tool.name} on ${on_string} Detail table"> | |
32 <filter>'detailed' in output_choice</filter> | |
33 </data> | |
34 <data name="output_detail_html" format="html" from_work_dir="output-detailRP.html" label="${tool.name} on ${on_string} Detail html"> | |
35 <filter>'detailed' in output_choice</filter> | |
36 </data> | |
37 </outputs> | |
38 <tests> | |
39 <test> | |
40 <param name="idc2" value="BilanEnrichiRP_Test1.tabular"/> | |
41 <param name="output_choice" value="detailed"/> | |
42 <output name="output_detail_tabular" file="BilanEnrichiRP_Test1_out_tab.tabular" ftype="tabular"/> | |
43 </test> | |
44 </tests> | |
45 <help><![CDATA[ | |
46 **What it does** | |
47 | |
48 The tool analyzes the observations made with the "Routier" or "Pedestre" protocols. | |
49 | |
50 **Arguments** | |
51 | |
52 - Input is an observation/participation file corrected by the tools Tadarida data cleaner and Tadarida identifications integration. | |
53 - Outputs are Summary and details raw tabulars, and html visualisations. | |
54 ]]></help> | |
55 <expand macro="vigiechiro_bibref" /> | |
56 </tool> |