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