Mercurial > repos > ecology > pampa_glmsp

annotate PAMPA_GLM_SP.xml @ 4:7a69e1c8ba46 draft default tip

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 65ab5b6fe84871db0fe18244d805cea19a44e830"
author ecology
date Sat, 26 Jun 2021 07:20:29 +0000
parents c12897ba5f83
children
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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"
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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
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18 $settings.rdata
0
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19 #else
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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20 'None'
2
6c14021f678e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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21 'false'
0
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22 #end if
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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23 'unitSp'
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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24 '$__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
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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"
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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"
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49 <param name="varint" value="4"/>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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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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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"
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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"
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59 </output>
0778efa9eb2e "planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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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"
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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"
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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"
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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"
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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 ===============================================================
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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 - Response variable among numeric or integer variables of the input file
0
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105
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106 - Explanatory 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**
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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
3
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122 +----------------------+--------------+---------+---------+-----+
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123 | observation.unit | species.code | metric1 | metric2 | ... |
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124 +======================+==============+=========+=========+=====+
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125 | year_locationID | species code | 2 | 0.4 | ... |
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126 +----------------------+--------------+---------+---------+-----+
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127 | ... | ... | ... | ... | ... |
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128 +----------------------+--------------+---------+---------+-----+
0
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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 | ... |
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134 +======+==========+==============+=========+=========+=====+
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135 | 2000 |locationID| species code | 2 | 0.4 | ... |
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136 +------+----------+--------------+---------+---------+-----+
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137 | ... | ... | ... | ... | ... | ... |
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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.
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141
4
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142 A tabular file with observation unit data which contains at least as much columns as used explanatory variables in addition with the 'observation.unit' column.
0
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143
4
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144 +-------------------+---------+--------+------------+-----+
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145 | observation.unit | site | year | habitat | ... |
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146 +===================+=========+========+============+=====+
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147 | year_locationID | site ID | 2000 | habitatID | ... |
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148 +-------------------+---------+--------+------------+-----+
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149 | ... | ... | ... | ... | ... |
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150 +-------------------+---------+--------+------------+-----+
0
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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
3
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158 Three text files :
0
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159
3
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160 - A first tabular 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
3
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164 - A third text file with ratings of your analysis based on several criterias.
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165
0
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166 |
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167
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168 **Source**
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169
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170 Derived from PAMPA scripts (https://wwz.ifremer.fr/pampa/Meth.-Outils/Outils) written by Yves Reecht.
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171
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172 ]]></help>
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173
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174 <expand macro="pampa_bibref" />
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175 </tool>