Mercurial > repos > ecology > vigiechiro_bilanenrichirp
view 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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<tool id="vigiechiro_bilanenrichirp" name="Advanced restitution: 'Routier'or 'Pedestre' protocols" version="@VERSION@"> <description>from Animal Detection on Acoustic Recordings</description> <macros> <import>vigiechiro_macros.xml</import> </macros> <expand macro="vigiechiro_bilanPF_bilanRP_requirements"/> <command detect_errors="exit_code"><![CDATA[ Rscript '$__tool_directory__/BilanEnrichiRP.R' '$idc2' '$__tool_directory__/refRPSeuil50.csv' '$__tool_directory__/SpeciesList.csv' && tail -n +2 output-summaryRP.html > tmp && mv tmp output-summaryRP.html && tail -n +2 output-detailRP.html > tmp && mv tmp output-detailRP.html ]]> </command> <inputs> <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"/> <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"> <option value="detailed" selected="true">detailed output</option> <option value="summarised">summarised output</option> </param> </inputs> <outputs> <data name="output_summary_tabular" format="tabular" from_work_dir="output-summaryRP.tabular" label="${tool.name} on ${on_string} Summary table"> <filter>'summarised' in output_choice</filter> </data> <data name="output_summary_html" format="html" from_work_dir="output-summaryRP.html" label="${tool.name} on ${on_string} Summary html"> <filter>'summarised' in output_choice</filter> </data> <data name="output_detail_tabular" format="tabular" from_work_dir="output-detailRP.tabular" label="${tool.name} on ${on_string} Detail table"> <filter>'detailed' in output_choice</filter> </data> <data name="output_detail_html" format="html" from_work_dir="output-detailRP.html" label="${tool.name} on ${on_string} Detail html"> <filter>'detailed' in output_choice</filter> </data> </outputs> <tests> <test> <param name="idc2" value="BilanEnrichiRP_Test1.tabular"/> <param name="output_choice" value="detailed"/> <output name="output_detail_tabular" file="BilanEnrichiRP_Test1_out_tab.tabular" ftype="tabular"/> </test> </tests> <help><![CDATA[ **What it does** The tool analyzes the observations made with the "Routier" or "Pedestre" protocols. **Arguments** - Input is an observation/participation file corrected by the tools Tadarida data cleaner and Tadarida identifications integration. - Outputs are Summary and details raw tabulars, and html visualisations. ]]></help> <expand macro="vigiechiro_bibref" /> </tool>