Mercurial > repos > ecology > pampa_glmsp
annotate PAMPA_GLM_SP.xml @ 4:7a69e1c8ba46 draft default tip
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 65ab5b6fe84871db0fe18244d805cea19a44e830"
author | ecology |
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date | Sat, 26 Jun 2021 07:20:29 +0000 |
parents | c12897ba5f83 |
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rev | line source |
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0
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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changeset
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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
parents:
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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
parents:
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3 <macros> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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4 <import>pampa_macros.xml</import> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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5 </macros> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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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"
ecology
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8 Rscript |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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9 '$__tool_directory__/FunctExeCalcGLMSpGalaxy.r' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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10 '$input_metric' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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11 '$input_unitobs' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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12 '$varint' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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13 '$varrep' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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14 '$varrand' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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15 'species.code' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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16 #if $settings.advanced=='advanced' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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17 $settings.distrib |
2
6c14021f678e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
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18 $settings.rdata |
0
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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19 #else |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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20 'None' |
2
6c14021f678e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
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1
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21 'false' |
0
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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22 #end if |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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23 'unitSp' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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24 '$__tool_directory__/FunctPAMPAGalaxy.r' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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25 '$output_summary' |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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26 '$output_recap' |
2
6c14021f678e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
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1
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27 #if $settings.advanced=='advanced' |
6c14021f678e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
parents:
1
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28 #if $settings.rdata=='true' |
6c14021f678e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
parents:
1
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29 '$output_GLM' |
6c14021f678e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
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1
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30 #end if |
6c14021f678e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
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1
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31 #end if |
0
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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32 ]]> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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33 </command> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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34 <inputs> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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35 <expand macro="pampa_input_GLM"/> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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36 <expand macro="pampa_var_GLM"/> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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37 <conditional name="settings"> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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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
parents:
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39 </conditional> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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40 </inputs> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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41 <outputs> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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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
parents:
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43 <expand macro="pampa_output_GLM"/> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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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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1
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46 <test expect_num_outputs="4"> |
0
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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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"
ecology
parents:
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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
parents:
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49 <param name="varint" value="4"/> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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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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1
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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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1
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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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1
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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
parents:
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55 <output name="output_summary"> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
parents:
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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"
ecology
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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
parents:
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60 <output name="output_recap"> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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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"
ecology
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65 <output name="output_rate"> |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
ecology
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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"
ecology
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71 <element name="GLM_Abalstel" ftype="Rdata"> |
6c14021f678e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
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72 <assert_contents> |
6c14021f678e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
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73 <has_size value="199219" delta="10000"/> |
6c14021f678e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
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74 </assert_contents> |
6c14021f678e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
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75 </element> |
6c14021f678e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
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76 <element name="GLM_Hemifasc" ftype="Rdata"> |
6c14021f678e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
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77 <assert_contents> |
6c14021f678e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
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78 <has_size value="202264" delta="10000"/> |
6c14021f678e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
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79 </assert_contents> |
6c14021f678e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
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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"
ecology
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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"
ecology
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84 </assert_contents> |
6c14021f678e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
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85 </element> |
6c14021f678e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
ecology
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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> |
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88 </tests> |
1
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit e8643d3d2e48d2ec7fcb2bd5abf77869a8687422"
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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
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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93 <help><![CDATA[ |
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94 =============================================================== |
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95 Compute GLM on population data with selected interest variables |
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96 =============================================================== |
0778efa9eb2e
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97 |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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98 **What it does** |
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99 |
0778efa9eb2e
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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 |
4
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104 - Response variable among numeric or integer variables of the input file |
0
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105 |
4
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106 - Explanatory variables among year, site and/or habitat |
0
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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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 |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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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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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit cd938a05cb066b16f2518159fa0ff5e3ed8a2b2b"
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122 +----------------------+--------------+---------+---------+-----+ |
c12897ba5f83
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit cd938a05cb066b16f2518159fa0ff5e3ed8a2b2b"
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123 | observation.unit | species.code | metric1 | metric2 | ... | |
c12897ba5f83
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit cd938a05cb066b16f2518159fa0ff5e3ed8a2b2b"
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124 +======================+==============+=========+=========+=====+ |
c12897ba5f83
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit cd938a05cb066b16f2518159fa0ff5e3ed8a2b2b"
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125 | year_locationID | species code | 2 | 0.4 | ... | |
c12897ba5f83
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit cd938a05cb066b16f2518159fa0ff5e3ed8a2b2b"
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126 +----------------------+--------------+---------+---------+-----+ |
c12897ba5f83
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit cd938a05cb066b16f2518159fa0ff5e3ed8a2b2b"
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127 | ... | ... | ... | ... | ... | |
c12897ba5f83
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit cd938a05cb066b16f2518159fa0ff5e3ed8a2b2b"
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128 +----------------------+--------------+---------+---------+-----+ |
0
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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129 |
0778efa9eb2e
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130 OR |
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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131 |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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132 +------+----------+--------------+---------+---------+-----+ |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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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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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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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 +------+----------+--------------+---------+---------+-----+ |
0778efa9eb2e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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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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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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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 |
4
7a69e1c8ba46
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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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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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143 |
4
7a69e1c8ba46
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 65ab5b6fe84871db0fe18244d805cea19a44e830"
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144 +-------------------+---------+--------+------------+-----+ |
7a69e1c8ba46
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 65ab5b6fe84871db0fe18244d805cea19a44e830"
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145 | observation.unit | site | year | habitat | ... | |
7a69e1c8ba46
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 65ab5b6fe84871db0fe18244d805cea19a44e830"
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146 +===================+=========+========+============+=====+ |
7a69e1c8ba46
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 65ab5b6fe84871db0fe18244d805cea19a44e830"
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147 | year_locationID | site ID | 2000 | habitatID | ... | |
7a69e1c8ba46
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 65ab5b6fe84871db0fe18244d805cea19a44e830"
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148 +-------------------+---------+--------+------------+-----+ |
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149 | ... | ... | ... | ... | ... | |
7a69e1c8ba46
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 65ab5b6fe84871db0fe18244d805cea19a44e830"
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150 +-------------------+---------+--------+------------+-----+ |
0
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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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151 |
2
6c14021f678e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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152 The site may represent the same entity as the location or represent an aggregation of several locations. |
6c14021f678e
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 3df1978827a91be30e815dee2ed83a92862d1b1c"
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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
c12897ba5f83
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158 Three text files : |
0
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159 |
3
c12897ba5f83
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160 - A first tabular file with GLM results. One analysis per species. |
0
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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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"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 07f1028cc764f920b1e6419c151f04ab4e3600fa"
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163 |
3
c12897ba5f83
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164 - A third text file with ratings of your analysis based on several criterias. |
c12897ba5f83
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit cd938a05cb066b16f2518159fa0ff5e3ed8a2b2b"
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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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parents:
diff
changeset
|
175 </tool> |