| Previous changeset 1:f9d76a46799a (2019-06-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc commit 69bd23adfce0944555888db6712266687276892e |
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modified:
spocc_occ.R spocc_occ.xml |
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added:
macro.xml |
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| diff -r f9d76a46799a -r f64b3c1a80a6 macro.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macro.xml Thu Jun 08 08:35:01 2023 +0000 |
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| @@ -0,0 +1,9 @@ +<macros> + <token name="@VERSION@">1.2.2</token> + <xml name="occ_requirements"> + <requirements> + <requirement type="package" version="@VERSION@">r-spocc</requirement> + <yield/> + </requirements> + </xml> +</macros> |
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| diff -r f9d76a46799a -r f64b3c1a80a6 spocc_occ.R --- a/spocc_occ.R Fri Jun 14 09:00:58 2019 -0400 +++ b/spocc_occ.R Thu Jun 08 08:35:01 2023 +0000 |
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| @@ -55,3 +55,4 @@ write.table(file="output.tab",results_data,sep="\t",row.names=FALSE) q('no') + |
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| diff -r f9d76a46799a -r f64b3c1a80a6 spocc_occ.xml --- a/spocc_occ.xml Fri Jun 14 09:00:58 2019 -0400 +++ b/spocc_occ.xml Thu Jun 08 08:35:01 2023 +0000 |
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| @@ -1,8 +1,10 @@ -<tool id="spocc_occ" name="Get species occurrences data" version="0.9.0"> - <description>from GBIF, ALA, iNAT and others</description> - <requirements> - <requirement type="package" version="0.9.0">r-spocc</requirement> - </requirements> +<tool id="spocc_occ" name="Get species occurrences data" version="@VERSION@"> + <description>from GBIF, OBIS, ALA, iNAT and others</description> + <macros> + <import>macro.xml</import> + </macros> + <expand macro="occ_requirements"> + </expand> <command detect_errors="exit_code"><![CDATA[ Rscript '$__tool_directory__/spocc_occ.R' '$sname' @@ -20,16 +22,13 @@ <option value="bison">Biodiversity Information Serving Our Nation : BISON</option> <option value="inat">INaturalist : INAT</option> <option value="ebird">eBbird</option> -<!-- - <option value="antweb">AntWeb</option> <option value="ala">Atlas of Living Australia : ALA</option> <option value="idigbio">Integrated Digitized Biocollections : iDigBio</option> <option value="obis">Oceanic Biogeographic Information System : OBIS</option> ---> <option value="ecoengine">Berkeley Ecoinformatics Engine : EcoEngine</option> <option value="vertnet">VertNet</option> </param> - <param name="limit" type="integer" label="Number of records to return" help="This is passed across all sources" value="500"/> + <param name="limit" type="integer" label="Number of records to return" help="This is passed across all sources. If you have an empty output you should try with a records value smaller." value="500" max="999999"/> </inputs> <outputs> <data name="output" format="tabular" from_work_dir="output.tab" label="Species occurences"/> @@ -48,6 +47,10 @@ </output> </test> </tests> + <edam_topics> + <edam_topic>topic_0610</edam_topic> + <edam_topic>topic_3050</edam_topic> + </edam_topics> <help><![CDATA[ =========================== Get species occurences data @@ -100,17 +103,14 @@ - VertNet http://vertnet.org/ -.. - AntWeb -.. https://www.antweb.org/ - -.. - Integrated Digitized Biocollections : iDigBio -.. https://www.idigbio.org/ + - Integrated Digitized Biocollections : iDigBio + https://www.idigbio.org/ -.. - Ocean Biogeographic Information System : OBIS -.. https://obis.org/ + - Ocean Biogeographic Information System : OBIS + https://obis.org/ -.. - Atlas of Living Australia : ALA -.. https://www.ala.org.au/. + - Atlas of Living Australia : ALA + https://www.ala.org.au/. Includes functionality for retrieving species occurrence data, and combining those data. @@ -124,3 +124,4 @@ Reference manual : https://cran.r-project.org/web/packages/spocc/spocc.pdf ]]></help> </tool> + |