comparison plot-trend.xml @ 0:58ecd15e6836 draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e

0:58ecd15e6836

<tool id="regionalgam_plot_trend" name="Plot abundance" version="@VERSION@">
    <description>with trend line</description>
    <macros>
        <import>regionalgam_macros.xml</import>
    </macros>
    <expand macro="rg_nlme_mass_requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$__tool_directory__/plot-trend.R' 
            '$ab_indices' '$gls_model'  
            '$output' 
            '$output_tsv' 
    ]]>
    </command>
    <inputs>
        <expand macro="rg_ab_indices"/>
        <expand macro="rg_gls_model"/>
    </inputs>
    <outputs>
        <data format="png" name="output" from_work_dir="output-plot-trend.png" />
        <data format="tabular" name="output_tsv" from_work_dir="s_trend.tsv" />
    </outputs>
    <tests>
        <test>
            <param name="ab_indices" value="s_data_index.tabular"/>
            <param name="gls_model" value="s_gls-adju_rda.rda"/>
            <output name="output_tsv" ftype="tabular">
                <assert_contents>
                    <has_line_matching expression="2003&#009;5.5699.*"/>
                    <has_line_matching expression="2004&#009;5.6221.*"/>
                    <has_line_matching expression="2005&#009;5.6915.*"/>
                    <has_line line="&quot;year&quot;&#009;&quot;collated index&quot;"/>
                    <has_n_columns n="2"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
==========================
Plot abundance trend 
==========================

This tool is an implementation of the plot_trend function from RegionalGAM package: https://github.com/RetoSchmucki/regionalGAM/

This function plot abundance and add a trend line, it is the year effect estimated in the model.

|

**Outputs**

Trend estimation plotted in an image png file, and raw values in a tabular file.

    ]]></help>
    <expand macro="rg_citation"/>
</tool>