Mercurial > repos > ecology > vigiechiro_bilanenrichirp
diff BilanEnrichiRPen.xml @ 0:c55e09a8b4c8 draft
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit d2de8e10c11bfa3b04729e59bba58e08d23b56aa
author | ecology |
---|---|
date | Wed, 13 Mar 2019 11:17:44 -0400 |
parents | |
children | be4e28da3919 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BilanEnrichiRPen.xml Wed Mar 13 11:17:44 2019 -0400 @@ -0,0 +1,56 @@ +<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>