Mercurial > repos > ecology > pampa_glmsp

annotate PAMPA_GLM_SP.xml @ 2:6c14021f678e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
author ecology
date Sun, 22 Nov 2020 18:40:40 +0000
parents e972fe2bffee
children c12897ba5f83
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
diff changeset
1 <tool id="pampa_glmsp" name="Compute GLM on population data" version="@VERSION@">
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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2 <description>Compute a GLM of your choice on population data</description>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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3 <macros>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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4 <import>pampa_macros.xml</import>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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5 </macros>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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6 <expand macro="GLM_requirements"/>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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7 <command detect_errors="exit_code"><![CDATA[
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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8 Rscript
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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9 '$__tool_directory__/FunctExeCalcGLMSpGalaxy.r'
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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10 '$input_metric'
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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11 '$input_unitobs'
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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12 '$varint'
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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13 '$varrep'
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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14 '$varrand'
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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15 'species.code'
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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16 #if $settings.advanced=='advanced'
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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17 $settings.distrib
2
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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18 $settings.rdata
0
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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19 #else
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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20 'None'
2
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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21 'false'
0
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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22 #end if
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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23 'unitSp'
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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24 '$__tool_directory__/FunctPAMPAGalaxy.r'
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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25 '$output_summary'
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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26 '$output_recap'
2
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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27 #if $settings.advanced=='advanced'
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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28 #if $settings.rdata=='true'
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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29 '$output_GLM'
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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30 #end if
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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31 #end if
0
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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32 ]]>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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33 </command>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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34 <inputs>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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35 <expand macro="pampa_input_GLM"/>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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36 <expand macro="pampa_var_GLM"/>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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37 <conditional name="settings">
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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38 <expand macro="pampa_advanced_params_select_GLM"/>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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39 </conditional>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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40 </inputs>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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41 <outputs>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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42 <data name="output_summary" from_work_dir="GLMSummary.tabular" format="tabular" label="GLM - Results from your population analysis on ${on_string}"/>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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43 <expand macro="pampa_output_GLM"/>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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44 </outputs>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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45 <tests>
2
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
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46 <test expect_num_outputs="4">
0
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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47 <param name="input_metric" value="Presence_absence_table_sansszcl_cropped.tabular"/>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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48 <param name="input_unitobs" value="Unitobs.tabular"/>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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49 <param name="varint" value="4"/>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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50 <param name="varrep" value="year,site,habitat"/>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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diff changeset
51 <param name="varrand" value="site"/>
2
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
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52 <param name="advanced" value="advanced"/>
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
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53 <param name="distrib" value="None"/>
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
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54 <param name="rdata" value="true"/>
0
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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55 <output name="output_summary">
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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56 <assert_contents>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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57 <has_n_lines n="4"/>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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58 </assert_contents>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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59 </output>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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60 <output name="output_recap">
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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61 <assert_contents>
2
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
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62 <has_n_lines n="606"/>
0
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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63 </assert_contents>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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64 </output>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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65 <output name="output_rate">
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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66 <assert_contents>
2
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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67 <has_n_lines n="45"/>
0
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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68 </assert_contents>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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69 </output>
2
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
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70 <output_collection name="output_GLM" type="list" count="3">
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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71 <element name="GLM_Abalstel" ftype="Rdata">
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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72 <assert_contents>
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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73 <has_size value="199219" delta="10000"/>
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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74 </assert_contents>
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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75 </element>
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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76 <element name="GLM_Hemifasc" ftype="Rdata">
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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77 <assert_contents>
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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78 <has_size value="202264" delta="10000"/>
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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79 </assert_contents>
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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80 </element>
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
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81 <element name="GLM_Zebrscop" ftype="Rdata">
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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82 <assert_contents>
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
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83 <has_size value="207311" delta="10000"/>
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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84 </assert_contents>
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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85 </element>
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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86 </output_collection>
0
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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87 </test>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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88 </tests>
1
e972fe2bffee "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit e8643d3d2e48d2ec7fcb2bd5abf77869a8687422"
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parents: 0
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89 <edam_topics>
e972fe2bffee "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit e8643d3d2e48d2ec7fcb2bd5abf77869a8687422"
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90 <edam_topic>topic_0610</edam_topic>
e972fe2bffee "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit e8643d3d2e48d2ec7fcb2bd5abf77869a8687422"
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91 <edam_topic>topic_3050</edam_topic>
e972fe2bffee "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit e8643d3d2e48d2ec7fcb2bd5abf77869a8687422"
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92 </edam_topics>
0
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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93 <help><![CDATA[
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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94 ===============================================================
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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95 Compute GLM on population data with selected interest variables
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96 ===============================================================
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97
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98 **What it does**
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99
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100 This tool from PAMPA toolsuite computes Generalized Linear Models on population data.
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101
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102 It allows user to choose composition of the model :
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103
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104 - Interest variable among numeric or integer variables of the input file
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105
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106 - Response variables among year, site and/or habitat
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107
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108 - Allocation of random effect on year and/or site
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109
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110 |
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111
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112 **Input description**
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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113
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114 A tabular file with population data. Must at least contain three or four columns depending on the case :
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115
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116 - ['year' and 'location'] or ['observation.unit']
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117
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118 - 'species.code'
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119
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120 - At least one population metric
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121
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122 +------------------+--------------+---------+---------+-----+
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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123 | observation.unit | species.code | metric1 | metric2 | ... |
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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124 +==================+==============+=========+=========+=====+
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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125 | site_yearID | species code | 2 | 0.4 | ... |
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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126 +------------------+--------------+---------+---------+-----+
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127 | ... | ... | ... | ... | ... |
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128 +------------------+--------------+---------+---------+-----+
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129
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130 OR
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131
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132 +------+----------+--------------+---------+---------+-----+
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133 | year | location | species.code | metric1 | metric2 | ... |
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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134 +======+==========+==============+=========+=========+=====+
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135 | 2000 |locationID| species code | 2 | 0.4 | ... |
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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136 +------+----------+--------------+---------+---------+-----+
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137 | ... | ... | ... | ... | ... | ... |
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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138 +------+----------+--------------+---------+---------+-----+
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139
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140 The first input may be extracted from the 'Calculate presence absence' tool.
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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141
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142 A tabular file with unitobs or location data which contains at least as much columns as used response variables and separation factor in addition with the 'observation.unit' or 'location' and 'species.code' column.
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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143
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144 +--------------------------------+--------------+---------+--------+------------+-----+
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145 | observation.unit OR location | species.code | site | year | habitat | ... |
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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146 +================================+==============+=========+========+============+=====+
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147 | site_yearID OR locationID | species code | site ID | 2000 | habitatID | ... |
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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148 +--------------------------------+--------------+---------+--------+------------+-----+
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149 | ... | ... | ... | ... | ... | ... |
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150 +--------------------------------+--------------+---------+--------+------------+-----+
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151
2
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152 The site may represent the same entity as the location or represent an aggregation of several locations.
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153
0
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154 |
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155
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156 **Output**
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157
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158 Two text files :
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159
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160 - A first text file with GLM results. One analysis per species.
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161
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162 - A second text file with simple statistics on the whole dataset.
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163
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164 |
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165
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166 **Source**
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167
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168 Derived from PAMPA scripts (https://wwz.ifremer.fr/pampa/Meth.-Outils/Outils) written by Yves Reecht.
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169
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170 ]]></help>
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171
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172 <expand macro="pampa_bibref" />
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173 </tool>