| Previous changeset 3:8d8aec182fb1 (2020-11-16) Next changeset 5:1ebb70b59037 (2021-06-26) |
|
Commit message:
"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit cd938a05cb066b16f2518159fa0ff5e3ed8a2b2b" |
|
modified:
FunctExeCalcPresAbsGalaxy.r FunctPAMPAGalaxy.r pampa_macros.xml test-data/Presence_absence_table_sansszcl_cropped.tabular |
| b |
| diff -r 8d8aec182fb1 -r 07b081730994 FunctExeCalcPresAbsGalaxy.r --- a/FunctExeCalcPresAbsGalaxy.r Mon Nov 16 11:02:09 2020 +0000 +++ b/FunctExeCalcPresAbsGalaxy.r Mon Apr 26 16:04:47 2021 +0000 |
| b |
| @@ -69,5 +69,5 @@ #Save dataframe in a tabular format filename_pres_abs <- "TabPresAbs.tabular" -write.table(res, filename_pres_abs, row.names = FALSE, sep = "\t", dec = ".", fileEncoding = "UTF-8") +write.table(res, filename_pres_abs, row.names = FALSE, quote = FALSE, sep = "\t", dec = ".", fileEncoding = "UTF-8") cat(paste("\nWrite table with presence/absence. \n--> \"", filename_pres_abs, "\"\n", sep = "")) |
| b |
| diff -r 8d8aec182fb1 -r 07b081730994 FunctPAMPAGalaxy.r --- a/FunctPAMPAGalaxy.r Mon Nov 16 11:02:09 2020 +0000 +++ b/FunctPAMPAGalaxy.r Mon Apr 26 16:04:47 2021 +0000 |
| b |
| @@ -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") && |
| b |
| diff -r 8d8aec182fb1 -r 07b081730994 pampa_macros.xml --- a/pampa_macros.xml Mon Nov 16 11:02:09 2020 +0000 +++ b/pampa_macros.xml Mon Apr 26 16:04:47 2021 +0000 |
| b |
| @@ -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"> |
| b |
| diff -r 8d8aec182fb1 -r 07b081730994 test-data/Presence_absence_table_sansszcl_cropped.tabular --- a/test-data/Presence_absence_table_sansszcl_cropped.tabular Mon Nov 16 11:02:09 2020 +0000 +++ b/test-data/Presence_absence_table_sansszcl_cropped.tabular Mon Apr 26 16:04:47 2021 +0000 |
| b |
| b'@@ -1,2134 +1,2134 @@\n-"location"\t"year"\t"species.code"\t"number"\t"number.max"\t"number.sd"\t"presence_absence"\t"observation.unit"\n-"AB_0008"\t"08"\t"Abalstel"\t0\t0\t0\t0\t"AB080008"\n-"AB_0015"\t"08"\t"Abalstel"\t0\t0\t0\t0\t"AB080015"\n-"AB_0027"\t"08"\t"Abalstel"\t0\t0\t0\t0\t"AB080027"\n-"AB_0031"\t"08"\t"Abalstel"\t0\t0\t0\t0\t"AB080031"\n-"AB_0037"\t"08"\t"Abalstel"\t0\t0\tNA\t0\t"AB080037"\n-"AB_0042"\t"08"\t"Abalstel"\t0\t0\tNA\t0\t"AB080042"\n-"AB_0057"\t"08"\t"Abalstel"\t0\t0\t0\t0\t"AB080057"\n-"AB_0076"\t"09"\t"Abalstel"\t0\t0\t0\t0\t"AB090076"\n-"AB_0081"\t"09"\t"Abalstel"\t0\t0\t0\t0\t"AB090081"\n-"AB_0095"\t"09"\t"Abalstel"\t0\t0\t0\t0\t"AB090095"\n-"AB_0097"\t"09"\t"Abalstel"\t0\t0\t0\t0\t"AB090097"\n-"AB_0098"\t"09"\t"Abalstel"\t0\t0\tNA\t0\t"AB090098"\n-"AB_0104"\t"09"\t"Abalstel"\t0\t0\t0\t0\t"AB090104"\n-"AB_0105"\t"09"\t"Abalstel"\t0\t0\t0\t0\t"AB090105"\n-"AB_0106"\t"09"\t"Abalstel"\t0\t0\tNA\t0\t"AB090106"\n-"AB_0120"\t"09"\t"Abalstel"\t0\t0\tNA\t0\t"AB090120"\n-"AB_0121"\t"09"\t"Abalstel"\t0\t0\t0\t0\t"AB090121"\n-"AB_0122"\t"09"\t"Abalstel"\t0\t0\t0\t0\t"AB090122"\n-"AB_0123"\t"09"\t"Abalstel"\t0\t0\t0\t0\t"AB090123"\n-"AB_0124"\t"09"\t"Abalstel"\t0\t0\tNA\t0\t"AB090124"\n-"AB_0125"\t"09"\t"Abalstel"\t0\t0\t0\t0\t"AB090125"\n-"AB_0126"\t"09"\t"Abalstel"\t0\t0\t0\t0\t"AB090126"\n-"AB_0127"\t"09"\t"Abalstel"\t0\t0\t0\t0\t"AB090127"\n-"AB_0132"\t"09"\t"Abalstel"\t0\t0\tNA\t0\t"AB090132"\n-"AB_0133"\t"09"\t"Abalstel"\t0\t0\t0\t0\t"AB090133"\n-"AB_0134"\t"09"\t"Abalstel"\t0\t0\t0\t0\t"AB090134"\n-"AB_0135"\t"09"\t"Abalstel"\t0\t0\t0\t0\t"AB090135"\n-"AB_0143"\t"09"\t"Abalstel"\t0\t0\tNA\t0\t"AB090143"\n-"AB_0148"\t"09"\t"Abalstel"\t0\t0\tNA\t0\t"AB090148"\n-"AB_0149"\t"09"\t"Abalstel"\t0\t0\t0\t0\t"AB090149"\n-"AB_0151"\t"09"\t"Abalstel"\t0\t0\t0\t0\t"AB090151"\n-"AB_0601"\t"09"\t"Abalstel"\t0\t0\t0\t0\t"AB090601"\n-"AB_0602"\t"09"\t"Abalstel"\t0\t0\t0\t0\t"AB090602"\n-"AB_0603"\t"09"\t"Abalstel"\t0\t0\tNA\t0\t"AB090603"\n-"AB_0001"\t"10"\t"Abalstel"\t0\t0\tNA\t0\t"AB100001"\n-"AB_0002"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100002"\n-"AB_0006"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100006"\n-"AB_0008"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100008"\n-"AB_0009"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100009"\n-"AB_0010"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100010"\n-"AB_0011"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100011"\n-"AB_0015"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100015"\n-"AB_0017"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100017"\n-"AB_0019"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100019"\n-"AB_0020"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100020"\n-"AB_0021"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100021"\n-"AB_0023"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100023"\n-"AB_0024"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100024"\n-"AB_0025"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100025"\n-"AB_0028"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100028"\n-"AB_0029"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100029"\n-"AB_0031"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100031"\n-"AB_0035"\t"10"\t"Abalstel"\t0\t0\tNA\t0\t"AB100035"\n-"AB_0036"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100036"\n-"AB_0038"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100038"\n-"AB_0042"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100042"\n-"AB_0046"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100046"\n-"AB_0047"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100047"\n-"AB_0048"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100048"\n-"AB_0049"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100049"\n-"AB_0052"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100052"\n-"AB_0055"\t"10"\t"Abalstel"\t0\t0\tNA\t0\t"AB100055"\n-"AB_0060"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100060"\n-"AB_0061"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100061"\n-"AB_0062"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100062"\n-"AB_0072"\t"10"\t"Abalstel"\t0\t0\tNA\t0\t"AB100072"\n-"AB_0077"\t"10"\t"Abalstel"\t0\t0\tNA\t0\t"AB100077"\n-"AB_0078"\t"10"\t"Abalstel"\t0\t0\tNA\t0\t"AB100078"\n-"AB_0079"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100079"\n-"AB_0081"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100081"\n-"AB_0082"\t"10"\t"Abalstel"\t0\t0\tNA\t0\t"AB100082"\n-"AB_0085"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100085"\n-"AB_0086"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100086"\n-"AB_0087"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100087"\n-"AB_0088"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100088"\n-"AB_0089"\t"10"\t"Abalstel"\t0\t0\tNA\t0\t"AB100089"\n-"AB_0090"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100090"\n-"AB_0091"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100091"\n-"AB_0092"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100092"\n-"AB_0093"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100093"\n-"AB_0094"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100094"\n-"AB_0095"\t"10"\t"Abalstel"\t0\t0\tNA\t0\t"AB100095"\n-"AB_0096"\t"10"\t"Abalstel"\t0\t0\t0\t0\t"AB100096"\n-"AB_0097"\t"10"\t"Abalstel"\t0\t0\t0\t0'..b'6\t1\tPA170014\n+PA_0015\t17\tZebrscop\t0\t0\tNA\t0\tPA170015\n+PA_0016\t17\tZebrscop\t1.33333333333333\t2\t0.577350269189626\t1\tPA170016\n+PA_0017\t17\tZebrscop\t0\t0\t0\t0\tPA170017\n+PA_0018\t17\tZebrscop\t0.5\t1\t0.707106781186548\t1\tPA170018\n+PA_0020\t17\tZebrscop\t1\t1\tNA\t1\tPA170020\n+PA_0022\t17\tZebrscop\t1\t1\t0\t1\tPA170022\n+PA_0025\t17\tZebrscop\t1\t1\tNA\t1\tPA170025\n+PA_0027\t17\tZebrscop\t1\t1\t0\t1\tPA170027\n+PA_0030\t17\tZebrscop\t2\t2\tNA\t1\tPA170030\n+PA_0039\t17\tZebrscop\t0\t0\t0\t0\tPA170039\n+PA_0041\t17\tZebrscop\t3\t4\t1\t1\tPA170041\n+PA_0042\t17\tZebrscop\t0\t0\t0\t0\tPA170042\n+PA_0043\t17\tZebrscop\t1.33333333333333\t2\t0.577350269189626\t1\tPA170043\n+PA_0044\t17\tZebrscop\t1\t1\tNA\t1\tPA170044\n+PA_0050\t17\tZebrscop\t1\t2\t1\t1\tPA170050\n+PA_0051\t17\tZebrscop\t0.5\t1\t0.707106781186548\t1\tPA170051\n+PA_0054\t17\tZebrscop\t0\t0\tNA\t0\tPA170054\n+PA_0055\t17\tZebrscop\t1\t1\tNA\t1\tPA170055\n+PA_0056\t17\tZebrscop\t4\t5\t1.73205080756888\t1\tPA170056\n+PA_0057\t17\tZebrscop\t9.66666666666667\t17\t6.35085296108588\t1\tPA170057\n+PA_0058\t17\tZebrscop\t18\t25\t6.08276253029822\t1\tPA170058\n+PA_0059\t17\tZebrscop\t0\t0\tNA\t0\tPA170059\n+PA_0060\t17\tZebrscop\t5.33333333333333\t8\t2.51661147842358\t1\tPA170060\n+PA_0066\t17\tZebrscop\t2\t2\tNA\t1\tPA170066\n+PA_0068\t17\tZebrscop\t1\t1\t0\t1\tPA170068\n+PA_0074\t17\tZebrscop\t0\t0\tNA\t0\tPA170074\n+PA_0079\t17\tZebrscop\t1\t1\tNA\t1\tPA170079\n+PA_0080\t17\tZebrscop\t5.66666666666667\t7\t1.52752523165195\t1\tPA170080\n+PA_0081\t17\tZebrscop\t2.5\t4\t2.12132034355964\t1\tPA170081\n+PA_0083\t17\tZebrscop\t1\t1\tNA\t1\tPA170083\n+PA_0084\t17\tZebrscop\t2.33333333333333\t3\t1.15470053837925\t1\tPA170084\n+PA_0088\t17\tZebrscop\t1.5\t2\t0.707106781186548\t1\tPA170088\n+PA_0091\t17\tZebrscop\t1.33333333333333\t2\t0.577350269189626\t1\tPA170091\n+PA_0093\t17\tZebrscop\t1\t1\t0\t1\tPA170093\n+PA_0094\t17\tZebrscop\t3\t3\tNA\t1\tPA170094\n+PA_0100\t17\tZebrscop\t0\t0\tNA\t0\tPA170100\n+PE_0007\t14\tZebrscop\t1\t1\t0\t1\tPE140007\n+PE_0025\t14\tZebrscop\t0\t0\tNA\t0\tPE140025\n+PE_0029\t14\tZebrscop\t0\t0\tNA\t0\tPE140029\n+PE_0031\t14\tZebrscop\t1\t1\t0\t1\tPE140031\n+PE_0033\t14\tZebrscop\t0\t0\t0\t0\tPE140033\n+PE_0035\t14\tZebrscop\t2.33333333333333\t3\t1.15470053837925\t1\tPE140035\n+PO_0001\t12\tZebrscop\t1\t1\tNA\t1\tPO120001\n+PO_0004\t12\tZebrscop\t1.5\t2\t0.707106781186548\t1\tPO120004\n+PO_0007\t12\tZebrscop\t2\t3\t1\t1\tPO120007\n+PO_0018\t12\tZebrscop\t1\t1\tNA\t1\tPO120018\n+PO_0028\t12\tZebrscop\t2\t3\t1.4142135623731\t1\tPO120028\n+PO_0045\t12\tZebrscop\t2.33333333333333\t3\t0.577350269189626\t1\tPO120045\n+PO_0048\t12\tZebrscop\t1\t1\tNA\t1\tPO120048\n+PO_0053\t12\tZebrscop\t1\t1\t0\t1\tPO120053\n+PO_0066\t12\tZebrscop\t1\t1\t0\t1\tPO120066\n+PO_0092\t12\tZebrscop\t6.16666666666667\t8.5\t2.25462487641145\t1\tPO120092\n+PO_0094\t12\tZebrscop\t1\t1\t0\t1\tPO120094\n+PO_0096\t12\tZebrscop\t2\t3\t1\t1\tPO120096\n+PO_0121\t12\tZebrscop\t5\t6\t1.4142135623731\t1\tPO120121\n+PO_0134\t12\tZebrscop\t0\t0\tNA\t0\tPO120134\n+PO_0136\t12\tZebrscop\t1\t1\tNA\t1\tPO120136\n+PO_0200\t12\tZebrscop\t2\t2\tNA\t1\tPO120200\n+PO_0203\t12\tZebrscop\t3.6\t4\t0.565685424949238\t1\tPO120203\n+PO_0205\t12\tZebrscop\t1\t1\tNA\t1\tPO120205\n+PO_0206\t12\tZebrscop\t1.33333333333333\t2\t0.577350269189626\t1\tPO120206\n+PO_0233\t12\tZebrscop\t2\t2\tNA\t1\tPO120233\n+RD_0219\t07\tZebrscop\t0\t0\t0\t0\tRD070219\n+RD_0230\t07\tZebrscop\t0\t0\tNA\t0\tRD070230\n+RD_0031\t08\tZebrscop\t0\t0\tNA\t0\tRD080031\n+RD_0103\t09\tZebrscop\t0\t0\tNA\t0\tRD090103\n+RD_0105\t09\tZebrscop\t0\t0\tNA\t0\tRD090105\n+RD_0108\t09\tZebrscop\t0\t0\tNA\t0\tRD090108\n+RD_0109\t09\tZebrscop\t0\t0\tNA\t0\tRD090109\n+RD_0107\t10\tZebrscop\t0\t0\tNA\t0\tRD100107\n+RL_0250\t07\tZebrscop\t1\t1\tNA\t1\tRL070250\n+RL_0145\t08\tZebrscop\t1\t1\t0\t1\tRL080145\n+RL_0078\t09\tZebrscop\t1.33333333333333\t2\t0.577350269189626\t1\tRL090078\n+RL_0089\t09\tZebrscop\t2\t2\t0\t1\tRL090089\n+RL_0093\t09\tZebrscop\t1\t1\t0\t1\tRL090093\n+RL_0066\t10\tZebrscop\t1\t1\tNA\t1\tRL100066\n+RL_0076\t10\tZebrscop\t1.33333333333333\t2\t0.577350269189626\t1\tRL100076\n+RS_0169\t07\tZebrscop\t2.33333333333333\t3\t0.577350269189626\t1\tRS070169\n+RS_0189\t07\tZebrscop\t1\t1\t0\t1\tRS070189\n+SI_0078\t07\tZebrscop\t1\t1\tNA\t1\tSI070078\n+SI_0079\t07\tZebrscop\t8.33333333333333\t12\t4.04145188432738\t1\tSI070079\n+SI_0080\t07\tZebrscop\t2\t3\t1.4142135623731\t1\tSI070080\n+SI_0082\t07\tZebrscop\t0\t0\tNA\t0\tSI070082\n+SI_0197\t07\tZebrscop\t0\t0\tNA\t0\tSI070197\n+SI_0222\t07\tZebrscop\t0\t0\tNA\t0\tSI070222\n+SI_0194\t08\tZebrscop\t0\t0\t0\t0\tSI080194\n+WA_0002\t14\tZebrscop\t1\t1\t0\t1\tWA140002\n' |