Mercurial > repos > ecology > regionalgam_ab_index
diff ab-index.xml @ 0:d0ee713d4758 draft default tip
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
author | ecology |
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date | Thu, 20 Jun 2019 04:05:06 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ab-index.xml Thu Jun 20 04:05:06 2019 -0400 @@ -0,0 +1,45 @@ +<tool id="regionalgam_ab_index" name="Abundance index" version="@VERSION@"> + <description>computation across species, sites and years</description> + <macros> + <import>regionalgam_macros.xml</import> + </macros> + <expand macro="rg_r_requirements"/> + <command detect_errors="exit_code"><![CDATA[ + Rscript '$__tool_directory__/ab-index.R' + '$__tool_directory__/dennis-gam-initial-functions.R' + '$count_file' '$input2' + '$output' + ]]> + </command> + <inputs> + <expand macro="rg_count_file"/> + <param format="tabular" name="input2" type="data" label="Regional expected pattern of abundance" help="Flight curve output, tabular file."/> + </inputs> + <outputs> + <data format="tabular" name="output" from_work_dir="data.index" /> + </outputs> + <tests> + <test> + <param name="count_file" value="gatekeeper_CM_200320042005"/> + <param name="input2" value="s_flight_curve_result.tabular"/> + <output name="output" file="s_data_index.tabular"/> + </test> + </tests> + <help><![CDATA[ +========================== +Compute abundance index +========================== + +This tool is an implementation of the abundance_index function from RegionalGAM package: https://github.com/RetoSchmucki/regionalGAM/ + +This function compute the Abundance Index across sites and years from your dataset and the regional flight curve. + +| + +**Outputs** + +The tool returns computed abundance indices in tabular format. + + ]]></help> + <expand macro="rg_citation"/> +</tool>