Mercurial > repos > ecology > regionalgam_plot_trend
comparison plot-trend.xml @ 0:a4ac846c28ab draft default tip
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
| author | ecology |
|---|---|
| date | Thu, 20 Jun 2019 04:01:18 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:a4ac846c28ab |
|---|---|
| 1 <tool id="regionalgam_plot_trend" name="Plot abundance" version="@VERSION@"> | |
| 2 <description>with trend line</description> | |
| 3 <macros> | |
| 4 <import>regionalgam_macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="rg_nlme_mass_requirements"/> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 Rscript '$__tool_directory__/plot-trend.R' | |
| 9 '$ab_indices' '$gls_model' | |
| 10 '$output' | |
| 11 '$output_tsv' | |
| 12 ]]> | |
| 13 </command> | |
| 14 <inputs> | |
| 15 <expand macro="rg_ab_indices"/> | |
| 16 <expand macro="rg_gls_model"/> | |
| 17 </inputs> | |
| 18 <outputs> | |
| 19 <data format="png" name="output" from_work_dir="output-plot-trend.png" /> | |
| 20 <data format="tabular" name="output_tsv" from_work_dir="s_trend.tsv" /> | |
| 21 </outputs> | |
| 22 <tests> | |
| 23 <test> | |
| 24 <param name="ab_indices" value="s_data_index.tabular"/> | |
| 25 <param name="gls_model" value="s_gls-adju_rda.rda"/> | |
| 26 <output name="output_tsv" ftype="tabular"> | |
| 27 <assert_contents> | |
| 28 <has_line_matching expression="2003	5.5699.*"/> | |
| 29 <has_line_matching expression="2004	5.6221.*"/> | |
| 30 <has_line_matching expression="2005	5.6915.*"/> | |
| 31 <has_line line=""year"	"collated index""/> | |
| 32 <has_n_columns n="2"/> | |
| 33 </assert_contents> | |
| 34 </output> | |
| 35 </test> | |
| 36 </tests> | |
| 37 <help><![CDATA[ | |
| 38 ========================== | |
| 39 Plot abundance trend | |
| 40 ========================== | |
| 41 | |
| 42 This tool is an implementation of the plot_trend function from RegionalGAM package: https://github.com/RetoSchmucki/regionalGAM/ | |
| 43 | |
| 44 This function plot abundance and add a trend line, it is the year effect estimated in the model. | |
| 45 | |
| 46 | | |
| 47 | |
| 48 **Outputs** | |
| 49 | |
| 50 Trend estimation plotted in an image png file, and raw values in a tabular file. | |
| 51 | |
| 52 ]]></help> | |
| 53 <expand macro="rg_citation"/> | |
| 54 </tool> |