| Previous changeset 2:6c14021f678e (2020-11-22) Next changeset 4:7a69e1c8ba46 (2021-06-26) |
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Commit message:
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit cd938a05cb066b16f2518159fa0ff5e3ed8a2b2b" |
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modified:
FunctExeCalcGLMSpGalaxy.r FunctPAMPAGalaxy.r PAMPA_GLM_SP.xml pampa_macros.xml test-data/Presence_absence_table_sansszcl_cropped.tabular |
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| diff -r 6c14021f678e -r c12897ba5f83 FunctExeCalcGLMSpGalaxy.r --- a/FunctExeCalcGLMSpGalaxy.r Sun Nov 22 18:40:40 2020 +0000 +++ b/FunctExeCalcGLMSpGalaxy.r Mon Apr 26 16:05:35 2021 +0000 |
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| @@ -204,4 +204,4 @@ tab <- glm_species(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") |
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| diff -r 6c14021f678e -r c12897ba5f83 FunctPAMPAGalaxy.r --- a/FunctPAMPAGalaxy.r Sun Nov 22 18:40:40 2020 +0000 +++ b/FunctPAMPAGalaxy.r Mon Apr 26 16:05:35 2021 +0000 |
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| @@ -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") && |
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| diff -r 6c14021f678e -r c12897ba5f83 PAMPA_GLM_SP.xml --- a/PAMPA_GLM_SP.xml Sun Nov 22 18:40:40 2020 +0000 +++ b/PAMPA_GLM_SP.xml Mon Apr 26 16:05:35 2021 +0000 |
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| @@ -119,13 +119,13 @@ - At least one population metric -+------------------+--------------+---------+---------+-----+ -| observation.unit | species.code | metric1 | metric2 | ... | -+==================+==============+=========+=========+=====+ -| site_yearID | species code | 2 | 0.4 | ... | -+------------------+--------------+---------+---------+-----+ -| ... | ... | ... | ... | ... | -+------------------+--------------+---------+---------+-----+ ++----------------------+--------------+---------+---------+-----+ +| observation.unit | species.code | metric1 | metric2 | ... | ++======================+==============+=========+=========+=====+ +| year_locationID | species code | 2 | 0.4 | ... | ++----------------------+--------------+---------+---------+-----+ +| ... | ... | ... | ... | ... | ++----------------------+--------------+---------+---------+-----+ OR @@ -139,15 +139,15 @@ The first input may be extracted from the 'Calculate presence absence' 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' and 'species.code' column. +A tabular file with observation unit data which contains at least as much columns as used response variables in addition with the 'observation.unit' and 'species.code' column. -+--------------------------------+--------------+---------+--------+------------+-----+ -| observation.unit OR location | species.code | site | year | habitat | ... | -+================================+==============+=========+========+============+=====+ -| site_yearID OR locationID | species code | site ID | 2000 | habitatID | ... | -+--------------------------------+--------------+---------+--------+------------+-----+ -| ... | ... | ... | ... | ... | ... | -+--------------------------------+--------------+---------+--------+------------+-----+ ++-------------------+--------------+---------+--------+------------+-----+ +| observation.unit | species.code | site | year | habitat | ... | ++===================+==============+=========+========+============+=====+ +| year_locationID | species code | site ID | 2000 | habitatID | ... | ++-------------------+--------------+---------+--------+------------+-----+ +| ... | ... | ... | ... | ... | ... | ++-------------------+--------------+---------+--------+------------+-----+ The site may represent the same entity as the location or represent an aggregation of several locations. @@ -155,12 +155,14 @@ **Output** -Two text files : +Three text files : -- A first text file with GLM results. One analysis per species. +- A first tabular file with GLM results. One analysis per species. - 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** |
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| diff -r 6c14021f678e -r c12897ba5f83 pampa_macros.xml --- a/pampa_macros.xml Sun Nov 22 18:40:40 2020 +0000 +++ b/pampa_macros.xml Mon Apr 26 16:05:35 2021 +0000 |
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| @@ -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"> |
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| diff -r 6c14021f678e -r c12897ba5f83 test-data/Presence_absence_table_sansszcl_cropped.tabular --- a/test-data/Presence_absence_table_sansszcl_cropped.tabular Sun Nov 22 18:40:40 2020 +0000 +++ b/test-data/Presence_absence_table_sansszcl_cropped.tabular Mon Apr 26 16:05:35 2021 +0000 |
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