| Previous changeset 5:5bd7ddd7601f (2020-11-16) Next changeset 7:c67ece97d4b1 (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:
CalculateCommunityMetrics.xml FunctExeCalcCommIndexesGalaxy.r FunctPAMPAGalaxy.r pampa_macros.xml test-data/Community_metrics_cropped.tabular |
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| diff -r 5bd7ddd7601f -r 2cd0a5a321c2 CalculateCommunityMetrics.xml --- a/CalculateCommunityMetrics.xml Mon Nov 16 11:02:24 2020 +0000 +++ b/CalculateCommunityMetrics.xml Mon Apr 26 16:05:03 2021 +0000 |
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| @@ -45,7 +45,7 @@ This tool from PAMPA toolsuite computes community metrics from abundance data: -- Specific richness +- Species richness / alpha diversity - Shannon index - Simpson index - Pielou index |
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| diff -r 5bd7ddd7601f -r 2cd0a5a321c2 FunctExeCalcCommIndexesGalaxy.r --- a/FunctExeCalcCommIndexesGalaxy.r Mon Nov 16 11:02:24 2020 +0000 +++ b/FunctExeCalcCommIndexesGalaxy.r Mon Apr 26 16:05:03 2021 +0000 |
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| @@ -136,5 +136,5 @@ #Save dataframe in a tabular format filename_comm <- "TabCommunityIndexes.tabular" -write.table(table_comm_indexes, filename_comm, row.names = FALSE, sep = "\t", dec = ".", fileEncoding = "UTF-8") +write.table(table_comm_indexes, filename_comm, row.names = FALSE, quote = FALSE, sep = "\t", dec = ".", fileEncoding = "UTF-8") cat(paste("\nWrite table with Community indexes. \n--> \"", filename_comm, "\"\n", sep = "")) |
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| diff -r 5bd7ddd7601f -r 2cd0a5a321c2 FunctPAMPAGalaxy.r --- a/FunctPAMPAGalaxy.r Mon Nov 16 11:02:24 2020 +0000 +++ b/FunctPAMPAGalaxy.r Mon Apr 26 16:05:03 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 5bd7ddd7601f -r 2cd0a5a321c2 pampa_macros.xml --- a/pampa_macros.xml Mon Nov 16 11:02:24 2020 +0000 +++ b/pampa_macros.xml Mon Apr 26 16:05:03 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 5bd7ddd7601f -r 2cd0a5a321c2 test-data/Community_metrics_cropped.tabular --- a/test-data/Community_metrics_cropped.tabular Mon Nov 16 11:02:24 2020 +0000 +++ b/test-data/Community_metrics_cropped.tabular Mon Apr 26 16:05:03 2021 +0000 |
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| b'@@ -1,712 +1,712 @@\n-"location"\t"year"\t"number"\t"species_richness"\t"simpson"\t"simpson_l"\t"shannon"\t"pielou"\t"hill"\t"observation.unit"\n-"AB_0008"\t"08"\t2.66666666666667\t1\t1\t0\t0\tNA\t0\t"AB080008"\n-"AB_0015"\t"08"\t3\t1\t1\t0\t0\tNA\t0\t"AB080015"\n-"AB_0027"\t"08"\t1.33333333333333\t1\t1\t0\t0\tNA\t0\t"AB080027"\n-"AB_0031"\t"08"\t1.33333333333333\t1\t1\t0\t0\tNA\t0\t"AB080031"\n-"AB_0037"\t"08"\t1\t1\t1\t0\t0\tNA\t0\t"AB080037"\n-"AB_0042"\t"08"\t1\t1\t1\t0\t0\tNA\t0\t"AB080042"\n-"AB_0057"\t"08"\t1\t1\t1\t0\t0\tNA\t0\t"AB080057"\n-"AB_0076"\t"09"\t1\t1\t1\t0\t0\tNA\t0\t"AB090076"\n-"AB_0081"\t"09"\t1\t1\t1\t0\t0\tNA\t0\t"AB090081"\n-"AB_0095"\t"09"\t2.33333333333333\t1\t1\t0\t0\tNA\t0\t"AB090095"\n-"AB_0097"\t"09"\t1\t1\t1\t0\t0\tNA\t0\t"AB090097"\n-"AB_0098"\t"09"\t1\t1\t1\t0\t0\tNA\t0\t"AB090098"\n-"AB_0104"\t"09"\t1.2\t1\t1\t0\t0\tNA\t0\t"AB090104"\n-"AB_0105"\t"09"\t1.33333333333333\t1\t1\t0\t0\tNA\t0\t"AB090105"\n-"AB_0106"\t"09"\t2\t1\t1\t0\t0\tNA\t0\t"AB090106"\n-"AB_0120"\t"09"\t1\t1\t1\t0\t0\tNA\t0\t"AB090120"\n-"AB_0121"\t"09"\t2.33333333333333\t1\t1\t0\t0\tNA\t0\t"AB090121"\n-"AB_0122"\t"09"\t1\t1\t1\t0\t0\tNA\t0\t"AB090122"\n-"AB_0123"\t"09"\t1.5\t1\t1\t0\t0\tNA\t0\t"AB090123"\n-"AB_0124"\t"09"\t1\t1\t1\t0\t0\tNA\t0\t"AB090124"\n-"AB_0125"\t"09"\t3.33333333333333\t1\t1\t0\t0\tNA\t0\t"AB090125"\n-"AB_0126"\t"09"\t4.33333333333333\t1\t1\t0\t0\tNA\t0\t"AB090126"\n-"AB_0127"\t"09"\t1.66666666666667\t1\t1\t0\t0\tNA\t0\t"AB090127"\n-"AB_0132"\t"09"\t1.5\t1\t1\t0\t0\tNA\t0\t"AB090132"\n-"AB_0133"\t"09"\t2\t1\t1\t0\t0\tNA\t0\t"AB090133"\n-"AB_0134"\t"09"\t2\t1\t1\t0\t0\tNA\t0\t"AB090134"\n-"AB_0135"\t"09"\t1\t1\t1\t0\t0\tNA\t0\t"AB090135"\n-"AB_0143"\t"09"\t1\t1\t1\t0\t0\tNA\t0\t"AB090143"\n-"AB_0148"\t"09"\t1\t1\t1\t0\t0\tNA\t0\t"AB090148"\n-"AB_0149"\t"09"\t3\t1\t1\t0\t0\tNA\t0\t"AB090149"\n-"AB_0151"\t"09"\t1.33333333333333\t1\t1\t0\t0\tNA\t0\t"AB090151"\n-"AB_0601"\t"09"\t1.66666666666667\t1\t1\t0\t0\tNA\t0\t"AB090601"\n-"AB_0602"\t"09"\t4.66666666666667\t2\t0.86734693877551\t0.13265306122449\t0.257318640543832\t0.371232326640876\t0.10255697699183\t"AB090602"\n-"AB_0603"\t"09"\t1\t1\t1\t0\t0\tNA\t0\t"AB090603"\n-"AB_0001"\t"10"\t2\t1\t1\t0\t0\tNA\t0\t"AB100001"\n-"AB_0002"\t"10"\t4.33333333333333\t1\t1\t0\t0\tNA\t0\t"AB100002"\n-"AB_0006"\t"10"\t2.33333333333333\t1\t1\t0\t0\tNA\t0\t"AB100006"\n-"AB_0008"\t"10"\t3.33333333333333\t1\t1\t0\t0\tNA\t0\t"AB100008"\n-"AB_0009"\t"10"\t1.5\t1\t1\t0\t0\tNA\t0\t"AB100009"\n-"AB_0010"\t"10"\t1.33333333333333\t1\t1\t0\t0\tNA\t0\t"AB100010"\n-"AB_0011"\t"10"\t1.66666666666667\t1\t1\t0\t0\tNA\t0\t"AB100011"\n-"AB_0015"\t"10"\t1\t1\t1\t0\t0\tNA\t0\t"AB100015"\n-"AB_0017"\t"10"\t3.33333333333333\t1\t1\t0\t0\tNA\t0\t"AB100017"\n-"AB_0019"\t"10"\t1.5\t1\t1\t0\t0\tNA\t0\t"AB100019"\n-"AB_0020"\t"10"\t2\t1\t1\t0\t0\tNA\t0\t"AB100020"\n-"AB_0021"\t"10"\t3\t1\t1\t0\t0\tNA\t0\t"AB100021"\n-"AB_0023"\t"10"\t5.33333333333333\t1\t1\t0\t0\tNA\t0\t"AB100023"\n-"AB_0024"\t"10"\t1.33333333333333\t1\t1\t0\t0\tNA\t0\t"AB100024"\n-"AB_0025"\t"10"\t1\t1\t1\t0\t0\tNA\t0\t"AB100025"\n-"AB_0028"\t"10"\t3.33333333333333\t1\t1\t0\t0\tNA\t0\t"AB100028"\n-"AB_0029"\t"10"\t7\t2\t0.909297052154195\t0.0907029478458048\t0.191444081957717\t0.276195427647939\t0.0748993922015743\t"AB100029"\n-"AB_0031"\t"10"\t1\t1\t1\t0\t0\tNA\t0\t"AB100031"\n-"AB_0035"\t"10"\t1\t1\t1\t0\t0\tNA\t0\t"AB100035"\n-"AB_0036"\t"10"\t2.66666666666667\t1\t1\t0\t0\tNA\t0\t"AB100036"\n-"AB_0038"\t"10"\t3\t1\t1\t0\t0\tNA\t0\t"AB100038"\n-"AB_0042"\t"10"\t1\t1\t1\t0\t0\tNA\t0\t"AB100042"\n-"AB_0046"\t"10"\t4\t1\t1\t0\t0\tNA\t0\t"AB100046"\n-"AB_0047"\t"10"\t2\t1\t1\t0\t0\tNA\t0\t"AB100047"\n-"AB_0048"\t"10"\t2.66666666666667\t1\t1\t0\t0\tNA\t0\t"AB100048"\n-"AB_0049"\t"10"\t1.66666666666667\t1\t1\t0\t0\tNA\t0\t"AB100049"\n-"AB_0052"\t"10"\t1\t1\t1\t0\t0\tNA\t0\t"AB100052"\n-"AB_0055"\t"10"\t1\t1\t1\t0\t0\tNA\t0\t"AB100055"\n-"AB_0060"\t"10"\t4.33333333333333\t1\t1\t0\t0\tNA\t0\t"AB100060"\n-"AB_0061"\t"10"\t2.66666666666667\t1\t1\t0\t0\tNA\t0\t"AB100061"\n-"AB_0062"\t"10"\t3.66666666666667\t2\t0.702479338842975\t0.297520661157025\t0.474139313057837\t0.684038435639042\t0.185182969156178\t"AB100062"\n-"AB_0072"\t"10"\t1\t1\t1\t0\t0\tNA\t0\t"AB100072"\n-"AB_0077"\t"10"\t1\t1\t1\t0\t0\tNA\t0\t"AB100077"\n-"AB_0078"\t"10"\t1\t1\t1\t0\t0\tNA\t0\t"AB100078"\n-"AB_0079"\t"10"\t1\t1\t1\t0\t0\tNA\t0\t"AB100079"\n-"AB_0081"\t"10"\t1\t1\t1\t0\t0\tNA\t0\t"AB100081"\n-"AB_0082"\t"10"\t2\t1\t1\t0\t0\tNA\t0\t"AB100082"\n-"AB_0085"\t"10"\t2\t1\t1\t0\t0\tNA\t0\t"AB100085"\n-"AB_0086"\t"10"\t3.33333333333333\t1\t1\t0\t0\tNA\t0\t"AB100086"\n-"AB_0087"\t"10"\t1.66666666666667\t1\t1\t0\t0\tNA\t0\t"AB100087"\n-"AB_0088"\t"10"\t2.33333333333333\t1\t1\t0\t0\tNA\t0\t"AB100088"\n-"AB_0089"\t"10"\t3\t1'..b'54489\t0.235170526217511\tPA170018\n+PA_0020\t17\t3\t2\t0.555555555555556\t0.444444444444444\t0.636514168294813\t0.918295834054489\t0.235170526217511\tPA170020\n+PA_0022\t17\t1\t1\t1\t0\t0\tNA\t0\tPA170022\n+PA_0025\t17\t1\t1\t1\t0\t0\tNA\t0\tPA1700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