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added EDAM ontology #41

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merged 4 commits into from
Jul 31, 2020
Merged

added EDAM ontology #41

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270d1a6
added EDAM ontology
Jul 22, 2020
76edb94
added info in CONTRIBUTING
Jul 22, 2020
aa8e805
fix coding style
Jul 23, 2020
de7f653
added info about EDAM popovers
Jul 23, 2020
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22 changes: 22 additions & 0 deletions CONTRIBUTING.md
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Expand Up @@ -33,6 +33,28 @@ Best practices for developing new tools are [https://galaxy-iuc-standards.readth
<when input="format" value="csv" format="csv" />
~~~

- Add [EDAM](https://ifb-elixirfr.github.io/edam-browser) ontology in your tool, for both topics and operations. Most climate tools will have:

~~~`bash`
<edam_topics>
<edam_topic>topic_3855</edam_topic>
<edam_topic>topic_3318</edam_topic>
</edam_topics>
~~~

- [Environmental science](https://ifb-elixirfr.github.io/edam-browser/#topic_3855) (topic 3855)
- [Physics](https://ifb-elixirfr.github.io/edam-browser/#topic_3318) (topic_3318)


- If you are using [firefox](https://www.mozilla.org/en-GB/firefox/all/#product-desktop-release), you can install [EDAM Popovers plugin](https://addons.mozilla.org/en-US/firefox/addon/edam-popovers/) to get the detailed information to EDAM terms.

![EDAM popovers](edam_popovers.png)

We may need to update all the tools later when additional topics will be added for geosciences.

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🥇 Beautiful doc! 🥇

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Would it be useful to also mention that whoever edits this stuff (in Firefox, or maybe also Chrome), can install the EDAM Popovers plugin?
image

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Excellent idea. I installed firefox on my laptop to get it; I did not managed to install it with chrome. And it is definitely great! Thanks!

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@annefou if you feel like it please add those tipps and instructions to IUC and any other repo that you find :)

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Yes. I'll add an issue in IUC and make a PR. Thanks for your suggestion.


- Do not forget to follow [Galaxy IUC coding style](https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html?highlight=order#coding-style).

## Test a tool with planemo

~~~`bash`
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7 changes: 7 additions & 0 deletions tools/climate-stripes/climate-stripes.xml
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@@ -1,5 +1,12 @@
<tool id="climate_stripes" name="climate stripes" version="1.0.1">
<description>from timeseries</description>
<edam_topics>
<edam_topic>topic_3855</edam_topic>
<edam_topic>topic_3318</edam_topic>
</edam_topics>
<edam_operations>
<edam_operation>operation_0337</edam_operation>
</edam_operations>
<requirements>
<requirement type="package" version="3">python</requirement>
<requirement type="package" version="3.1.1">matplotlib</requirement>
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9 changes: 9 additions & 0 deletions tools/essential_climate_variables/essential_climate_variables.xml
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@@ -1,5 +1,14 @@
<tool id="cds_essential_variability" name="Copernicus Essential Climate Variables" version="0.1.4">
<description>for assessing climate variability</description>
<edam_topics>
<edam_topic>topic_3855</edam_topic>
<edam_topic>topic_3318</edam_topic>
</edam_topics>
<edam_operations>
<edam_operation>operation_2422</edam_operation>
<edam_operation>operation_3357</edam_operation>
<edam_operation>operation_0335</edam_operation>
</edam_operations>
<requirements>
<requirement type="package" version="3">python</requirement>
<requirement type="package" version="0.1.4">cdsapi</requirement>
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9 changes: 9 additions & 0 deletions tools/mean-per-zone/mean-per-zone.xml
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@@ -1,5 +1,14 @@
<tool id="mean_per_zone" name="zonal statistics" version="0.2.0">
<description>over each area</description>
<edam_topics>
<edam_topic>topic_3855</edam_topic>
<edam_topic>topic_3318</edam_topic>
</edam_topics>
<edam_operations>
<edam_operation>operation_2238</edam_operation>
<edam_operation>operation_3432</edam_operation>
<edam_operation>operation_0573</edam_operation>
</edam_operations>
<requirements>
<requirement type="package" version="3">python</requirement>
<requirement type="package" version="0.13.1">rasterstats</requirement>
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7 changes: 7 additions & 0 deletions tools/psy-maps/psy-maps.xml
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@@ -1,5 +1,12 @@
<tool id="psy_maps" name="map plot" version="1.2.1">
<description>gridded (lat/lon) netCDF data</description>
<edam_topics>
<edam_topic>topic_3855</edam_topic>
<edam_topic>topic_3318</edam_topic>
</edam_topics>
<edam_operations>
<edam_operation>operation_0573</edam_operation>
</edam_operations>
<requirements>
<requirement type="package" version="3">python</requirement>
<requirement type="package" version="1.2.1">psyplot</requirement>
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9 changes: 9 additions & 0 deletions tools/shift-longitudes/shift-longitudes.xml
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@@ -1,5 +1,14 @@
<tool id="shyft_longitudes" name="shift longitudes" version="0.1.0">
<description>from netCDF data</description>
<edam_topics>
<edam_topic>topic_3855</edam_topic>
<edam_topic>topic_3318</edam_topic>
</edam_topics>
<edam_operations>
<edam_operation>operation_3096</edam_operation>
<edam_operation>operation_3438</edam_operation>
<edam_operation>operation_3434</edam_operation>
</edam_operations>
<requirements>
<requirement type="package" version="3.6.7">python</requirement>
<requirement type="package" version="1.4.1">netcdf4</requirement>
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