Mercurial > repos > ecology > obisindicators
changeset 1:d7b6ff32d072 draft
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit d1d3e8640457c30349b842ea05de64b9312890f4
| author | ecology |
|---|---|
| date | Wed, 25 Jan 2023 16:01:52 +0000 |
| parents | 1015a0070bac |
| children | 01e08ae72a98 |
| files | macro.xml obisindicators.r obisindicators.xml |
| diffstat | 3 files changed, 8 insertions(+), 4 deletions(-) [+] |
line wrap: on
line diff
--- a/macro.xml Thu Dec 29 13:05:04 2022 +0000 +++ b/macro.xml Wed Jan 25 16:01:52 2023 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION@">0.0.1</token> + <token name="@VERSION@">0.0.2</token> <xml name="requirements"> <requirements> <requirement type="package" version="4.2.2">r-base</requirement>
--- a/obisindicators.r Thu Dec 29 13:05:04 2022 +0000 +++ b/obisindicators.r Wed Jan 25 16:01:52 2023 +0000 @@ -32,9 +32,10 @@ spe <- as.numeric(args[6]) rec <- as.numeric(args[7]) crs <- as.numeric(args[8]) - source(args[9]) + reso <- as.numeric(args[9]) source(args[10]) source(args[11]) + source(args[12]) } if (hr == "false") { @@ -63,7 +64,7 @@ #Create a discrete global grid #Create an ISEA discrete global grid of resolution 9 using the dggridR package: -dggs <- dggridR::dgconstruct(projection = "ISEA", topology = "HEXAGON", res = 9) +dggs <- dggridR::dgconstruct(projection = "ISEA", topology = "HEXAGON", res = reso) #Then assign cell numbers to the occurrence data occ$cell <- dggridR::dgGEO_to_SEQNUM(dggs, occ$decimalLongitude, occ$decimalLatitude)[["seqnum"]]
--- a/obisindicators.xml Thu Dec 29 13:05:04 2022 +0000 +++ b/obisindicators.xml Wed Jan 25 16:01:52 2023 +0000 @@ -31,6 +31,7 @@ '$species' '$records' '$type' + '$resolution' '$__tool_directory__/analyze.r' '$__tool_directory__/visualize.r' '$__tool_directory__/data.r' @@ -41,8 +42,8 @@ <inputs> <expand macro="SRS_input"/> <param name="separator" type="select" display="radio" label="What character is the separator in your data? (Mostlikely a comma for a csv file and t for a tabular)"> + <option value="t">Tabulator (\t)</option> <option value=",">Comma (,)</option> - <option value="t">Tabulator (\t)</option> </param> <param name="longitude" label="Select column containing the decimal value of the longitude " type="data_column" data_ref="input" numerical="true" use_header_names="true"/> <param name="latitude" label="Select column containing the decimal value of the latitude " type="data_column" data_ref="input" numerical="true" use_header_names="true"/> @@ -52,6 +53,7 @@ <option value="0">Robinson projection</option> <option value="4326">Geographic projection</option> </param> + <param name="resolution" label="Write a number between 1 and 30" type="text" data_ref="input" help="We strongly advise to stay below 15 or else you won't see a thing. The bigger your dataset is the smaller the resolution should be."/> </inputs> <outputs> <data name="output_index" from_work_dir="Index.csv" format="csv" label="Index"> @@ -70,6 +72,7 @@ <param name="species" value="c3: species"/> <param name="records" value="c5: records"/> <param name="type" value="0"/> + <param name="resolution" value="9"/> <output name="output_index" value="Index.csv"/> <output_collection name="plots" type="list" count="5"> <element name="ES_50" ftype="png">