Mercurial > repos > ecology > pampa_glmcomm
changeset 5:8db02073b671 draft
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit cd938a05cb066b16f2518159fa0ff5e3ed8a2b2b"
author | ecology |
---|---|
date | Mon, 26 Apr 2021 16:05:19 +0000 |
parents | 44b9069775ca |
children | b40fecef616b |
files | FunctExeCalcGLMGalaxy.r FunctPAMPAGalaxy.r PAMPA_GLM.xml pampa_macros.xml test-data/Community_metrics_cropped.tabular |
diffstat | 5 files changed, 738 insertions(+), 734 deletions(-) [+] |
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--- a/FunctExeCalcGLMGalaxy.r Sun Nov 22 18:40:23 2020 +0000 +++ b/FunctExeCalcGLMGalaxy.r Mon Apr 26 16:05:19 2021 +0000 @@ -257,4 +257,4 @@ tab <- glm_community(metrique = metric, list_fact = list_fact, list_rand = list_rand, fact_ana = fact_ana, distrib = distrib, tab_metrics = obs, tab_metrique = aggreg, tab_unitobs = tab_unitobs, nb_name = "number") -write.table(tab, "GLMSummary.tabular", row.names = FALSE, sep = "\t", dec = ".", fileEncoding = "UTF-8") +write.table(tab, "GLMSummary.tabular", row.names = FALSE, quote = FALSE, sep = "\t", dec = ".", fileEncoding = "UTF-8")
--- a/FunctPAMPAGalaxy.r Sun Nov 22 18:40:23 2020 +0000 +++ b/FunctPAMPAGalaxy.r Mon Apr 26 16:05:19 2021 +0000 @@ -1481,7 +1481,7 @@ ## Open file : f_ile <- file(description = filename, - open = "w", encoding = "latin1") + open = "w", encoding = "UTF-8") ## if error : on.exit(if (exists("filename") &&
--- a/PAMPA_GLM.xml Sun Nov 22 18:40:23 2020 +0000 +++ b/PAMPA_GLM.xml Mon Apr 26 16:05:19 2021 +0000 @@ -34,7 +34,7 @@ </command> <inputs> <expand macro="pampa_input_GLM"/> - <param name="sep" type="data_column" data_ref="input_unitobs" force_select="false" label="Separation factor of your analysis from unitobs file" help= "Choose the field of the separation factor, for each level of this factor, one GLM will be computed."/> + <param name="sep" type="data_column" data_ref="input_unitobs" use_header_names="true" force_select="false" label="Separation factor of your analysis from unitobs file" help= "Choose the field of the separation factor, for each level of this factor, one GLM will be computed."/> <expand macro="pampa_var_GLM"/> <conditional name="settings"> <expand macro="pampa_advanced_params_select_GLM"/> @@ -110,6 +110,8 @@ - Allocation of random effect on year and/or site +- (optional) Separation factor to compute several GLMs + | **Input description** @@ -120,13 +122,13 @@ - At least one community metric -+------------------+---------+---------+-----+ -| observation.unit | metric1 | metric2 | ... | -+==================+=========+=========+=====+ -| site_yearID | 2 | 0.4 | ... | -+------------------+---------+---------+-----+ -| ... | ... | ... | ... | -+------------------+---------+---------+-----+ ++----------------------+---------+---------+-----+ +| observation.unit | metric1 | metric2 | ... | ++======================+=========+=========+=====+ +| year_locationID | 2 | 0.4 | ... | ++----------------------+---------+---------+-----+ +| ... | ... | ... | ... | ++----------------------+---------+---------+-----+ OR @@ -140,15 +142,15 @@ The first input may be extracted from the 'Calculate community metrics' tool. -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' column. +A tabular file with observation unit data which contains at least as much columns as used response variables and separation factor in addition with the 'observation.unit' column. -+--------------------------------+---------+--------+------------+-----+ -| observation.unit OR location | site | year | habitat | ... | -+================================+=========+========+============+=====+ -| site_yearID OR locationID | site ID | 2000 | habitatID | ... | -+--------------------------------+---------+--------+------------+-----+ -| ... | ... | ... | ... | ... | -+--------------------------------+---------+--------+------------+-----+ ++----------------------+---------+--------+------------+-----+ +| observation.unit | site | year | habitat | ... | ++======================+=========+========+============+=====+ +| year_locationID | site ID | 2000 | habitatID | ... | ++----------------------+---------+--------+------------+-----+ +| ... | ... | ... | ... | ... | ++----------------------+---------+--------+------------+-----+ The site may represent the same entity as the location or represent an aggregation of several locations @@ -156,12 +158,14 @@ **Output** -Two text files : +Three text files : -- A first text file with GLM results. When a separation factor is selected, one analysis is computed for every level and the last analysis is on the whole dataset. +- A first tabular file with GLM results. When a separation factor is selected, one analysis is computed for every level and the last analysis is on the whole dataset. - A second text file with simple statistics on the whole dataset. +- A third text file with ratings of your analysis based on several criterias. + | **Source**
--- a/pampa_macros.xml Sun Nov 22 18:40:23 2020 +0000 +++ b/pampa_macros.xml Mon Apr 26 16:05:19 2021 +0000 @@ -15,7 +15,7 @@ </xml> <xml name="Plot_requirements"> <requirements> - <requirement type="package" version="3.1.1">r-ggplot2</requirement> + <requirement type="package" version="3.3.3">r-ggplot2</requirement> <requirement type="package" version="1.3_25">r-boot</requirement> </requirements> </xml> @@ -54,7 +54,7 @@ <xml name="pampa_input_GLM"> <param name="input_metric" type="data" format="tabular" label="Input metrics file" help="Metrics data file, with location, year, and metrics informations that can be used as interest variable."/> <param name="input_unitobs" type="data" format="tabular" label="Unitobs informations file" help="Unitobs file, with all informations available about unitobs."/> - <param name="varint" type="data_column" data_ref="input_metric" label="Interest variable from metrics file" help= "Choose the field of the interest variable."/> + <param name="varint" type="data_column" data_ref="input_metric" use_header_names="true" label="Interest variable from metrics file" help= "Choose the field of the interest variable."/> </xml> <xml name="pampa_var_GLM"> <param name="varrep" type="select" label="Response variables" help= "Choose the response variables you want to include in your analysis." multiple="true">
--- a/test-data/Community_metrics_cropped.tabular Sun Nov 22 18:40:23 2020 +0000 +++ b/test-data/Community_metrics_cropped.tabular Mon Apr 26 16:05:19 2021 +0000 @@ -1,712 +1,712 @@ -"location" "year" "number" "species_richness" "simpson" "simpson_l" "shannon" "pielou" "hill" "observation.unit" -"AB_0008" "08" 2.66666666666667 1 1 0 0 NA 0 "AB080008" -"AB_0015" "08" 3 1 1 0 0 NA 0 "AB080015" -"AB_0027" "08" 1.33333333333333 1 1 0 0 NA 0 "AB080027" -"AB_0031" "08" 1.33333333333333 1 1 0 0 NA 0 "AB080031" -"AB_0037" "08" 1 1 1 0 0 NA 0 "AB080037" -"AB_0042" "08" 1 1 1 0 0 NA 0 "AB080042" -"AB_0057" "08" 1 1 1 0 0 NA 0 "AB080057" -"AB_0076" "09" 1 1 1 0 0 NA 0 "AB090076" -"AB_0081" "09" 1 1 1 0 0 NA 0 "AB090081" -"AB_0095" "09" 2.33333333333333 1 1 0 0 NA 0 "AB090095" -"AB_0097" "09" 1 1 1 0 0 NA 0 "AB090097" -"AB_0098" "09" 1 1 1 0 0 NA 0 "AB090098" -"AB_0104" "09" 1.2 1 1 0 0 NA 0 "AB090104" -"AB_0105" "09" 1.33333333333333 1 1 0 0 NA 0 "AB090105" -"AB_0106" "09" 2 1 1 0 0 NA 0 "AB090106" -"AB_0120" "09" 1 1 1 0 0 NA 0 "AB090120" -"AB_0121" "09" 2.33333333333333 1 1 0 0 NA 0 "AB090121" -"AB_0122" "09" 1 1 1 0 0 NA 0 "AB090122" -"AB_0123" "09" 1.5 1 1 0 0 NA 0 "AB090123" -"AB_0124" "09" 1 1 1 0 0 NA 0 "AB090124" -"AB_0125" "09" 3.33333333333333 1 1 0 0 NA 0 "AB090125" -"AB_0126" "09" 4.33333333333333 1 1 0 0 NA 0 "AB090126" -"AB_0127" "09" 1.66666666666667 1 1 0 0 NA 0 "AB090127" -"AB_0132" "09" 1.5 1 1 0 0 NA 0 "AB090132" -"AB_0133" "09" 2 1 1 0 0 NA 0 "AB090133" -"AB_0134" "09" 2 1 1 0 0 NA 0 "AB090134" -"AB_0135" "09" 1 1 1 0 0 NA 0 "AB090135" -"AB_0143" "09" 1 1 1 0 0 NA 0 "AB090143" -"AB_0148" "09" 1 1 1 0 0 NA 0 "AB090148" -"AB_0149" "09" 3 1 1 0 0 NA 0 "AB090149" -"AB_0151" "09" 1.33333333333333 1 1 0 0 NA 0 "AB090151" -"AB_0601" "09" 1.66666666666667 1 1 0 0 NA 0 "AB090601" -"AB_0602" "09" 4.66666666666667 2 0.86734693877551 0.13265306122449 0.257318640543832 0.371232326640876 0.10255697699183 "AB090602" -"AB_0603" "09" 1 1 1 0 0 NA 0 "AB090603" 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