Mercurial > repos > siwaa > carboseq_s
changeset 15:de71663fbce4 draft
"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/a1d5502ae76ad46070a072641c73b7a51d21c82f/toos/CarboSeqSimulator commit a1d5502ae76ad46070a072641c73b7a51d21c82f-dirty"
| author | siwaa |
|---|---|
| date | Tue, 10 Dec 2024 09:14:52 +0000 |
| parents | e455667fe22f |
| children | 5ed871d666b4 |
| files | carboseqSimulator.xml carboseqSplit.xml run.r test-data/input/40Sites/40Sites.zip |
| diffstat | 4 files changed, 81 insertions(+), 12 deletions(-) [+] |
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--- a/carboseqSimulator.xml Fri Sep 20 09:00:02 2024 +0000 +++ b/carboseqSimulator.xml Tue Dec 10 09:14:52 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.16"> +<tool id="CarboSeqSimulator" name="CarboSeqSimulator" version="1.0.17"> <description>To run the CarboSeq simulator</description> <requirements> <container type="singularity">docker://registry.forgemia.inra.fr/csopra/csopralibs:main</container> @@ -36,7 +36,7 @@ <param name="semantifier" value="modeltoolbox_sem_local" /> <output name="output" ftype="rdata" > <assert_contents> - <has_size value="1202" negate="false" /> + <has_size value="1334" negate="false" /> <has_size value="0" negate="true" /> </assert_contents> </output> @@ -46,7 +46,7 @@ <param name="semantifier" value="modeltoolbox_sem_remote" /> <output name="output" ftype="rdata" > <assert_contents> - <has_size value="1202" negate="false" /> + <has_size value="1334" negate="false" /> <has_size value="0" negate="true" /> </assert_contents> </output>
--- a/carboseqSplit.xml Fri Sep 20 09:00:02 2024 +0000 +++ b/carboseqSplit.xml Tue Dec 10 09:14:52 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="CarboSeqSplit" name="CarboSeqSplit" version="1.0.3"> +<tool id="CarboSeqSplit" name="CarboSeqSplit" version="1.0.4"> <description>To split input data of CarboSeq</description> <requirements> <container type="singularity">docker://registry.forgemia.inra.fr/carboseq/record-projet-carboseq:latest</container> @@ -16,8 +16,78 @@ <discover_datasets pattern="__name_and_ext__" directory="outputs"/> </collection> </outputs> -<tests> -</tests> + <tests> + <test> + <param name="inputFile" value="input/40Sites/40Sites.zip" /> + <param name="chunkSize" value="10" /> + <output_collection name="splited" type="list" count="4"> + <element name="input_1"> + <assert_contents> + <has_archive_member path="crop.csv"> + <has_text text="ID,NUM,CROP" /> + <has_n_lines n="201" /> + </has_archive_member> + <has_archive_member path="soil.csv"> + <has_text text="ID,LAT" /> + <has_n_lines n="11" /> + </has_archive_member> + <has_archive_member path="units.csv"> + <has_text text="ID,NUM,CROP" /> + <has_n_lines n="81" /> + </has_archive_member> + </assert_contents> + </element> + <element name="input_2"> + <assert_contents> + <has_archive_member path="crop.csv"> + <has_text text="ID,NUM,CROP" /> + <has_n_lines n="201" /> + </has_archive_member> + <has_archive_member path="soil.csv"> + <has_text text="ID,LAT" /> + <has_n_lines n="11" /> + </has_archive_member> + <has_archive_member path="units.csv"> + <has_text text="ID,NUM,CROP" /> + <has_n_lines n="81" /> + </has_archive_member> + </assert_contents> + </element> + <element name="input_3"> + <assert_contents> + <has_archive_member path="crop.csv"> + <has_text text="ID,NUM,CROP" /> + <has_n_lines n="201" /> + </has_archive_member> + <has_archive_member path="soil.csv"> + <has_text text="ID,LAT" /> + <has_n_lines n="11" /> + </has_archive_member> + <has_archive_member path="units.csv"> + <has_text text="ID,NUM,CROP" /> + <has_n_lines n="81" /> + </has_archive_member> + </assert_contents> + </element> + <element name="input_4"> + <assert_contents> + <has_archive_member path="crop.csv"> + <has_text text="ID,NUM,CROP" /> + <has_n_lines n="201" /> + </has_archive_member> + <has_archive_member path="soil.csv"> + <has_text text="ID,LAT" /> + <has_n_lines n="11" /> + </has_archive_member> + <has_archive_member path="units.csv"> + <has_text text="ID,NUM,CROP" /> + <has_n_lines n="81" /> + </has_archive_member> + </assert_contents> + </element> + </output_collection> + </test> + </tests> <help> the CarboSeq CarboseqSimulator tool ===================================
--- a/run.r Fri Sep 20 09:00:02 2024 +0000 +++ b/run.r Tue Dec 10 09:14:52 2024 +0000 @@ -157,12 +157,11 @@ } ppi <- list( - weatherRetrievalMethod = "service", - srcDir = srcDir, - # srcDirOutput = srcDirOutput, - doSemantify = DS, - weatherRetrievalURL = "https://coby.infosol.inrae.fr:8080/climate", - semantifierServiceURL = url + weatherRetrievalMethod = "service", + srcDir = srcDir, + doSemantify = DS, + weatherRetrievalURL = "https://coby.infosol.inrae.fr:8080/spatial-data/temporal/climate", + semantifierServiceURL = url )