view mainglm_group.xml @ 2:8f953c35c787 draft default tip

"planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit d49a4da1ffac1f33a15fdb7ae98827d0034a7879"

<tool id="stoceps_glm_group" name="Estimate temporal population variation" version="@VERSION@">
    <description>by specialization group</description>
    <macros>
        <import>stoceps_macros.xml</import>
    </macros>
    <expand macro="mainglm_requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        Rscript 
         '$__tool_directory__/ExeMainglmParGroupGalaxy.r' 
         '$input_y_var'
         '$input_glob_tendencies'
         '$inputtabSpecies'
         'mainglm_group'
         #if $settings.advanced=='advanced' 
             $settings.sp_code
         #else
             ''
         #end if
         '$__tool_directory__/FunctTrendSTOCGalaxy.r'
         '$__tool_directory__/biais.tabular'
         
        '$data_group'
        '$year_var_group'
        '$glob_tend_group'
    ]]>
    </command>
    <inputs>
        <param name="input_y_var" type="data" format="tabular" label="Yearly variation dataset" help="Output from the 'Estimate temporal population evoution by species' tool."/>
        <param name="input_glob_tendencies" type="data" format="tabular" label="Global tendencies dataset" help="Output from the 'Estimate temporal population evoution by species' tool."/>
        <param name="inputtabSpecies" type="data" format="tabular" label="Species file" help="Input species tabular file, with 5 columns (species ID, species name, species scientific name, specialization status)." />
        <conditional name="settings">
            <expand macro="stoceps_advanced_params_select"/>
            <when value="advanced">
                <param name="sp_code" type="select" label="Filter species to exclude" help="Create a subsample by selecting the species codes you don't want to use." multiple="true" optional="true">
                    <options from_dataset="input_glob_tendencies">
                        <column name="value" index="1"/>
                        <filter type="unique_value" name="espece" column="1"/>
                    </options>
                    <sanitizer>
                        <valid initial="string.printable">
                            <remove value="&quot;"/>
                        </valid>
                    </sanitizer>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="data_group" from_work_dir="Output/mainglm_group/donneesGroupes_mainglm_group.tabular" format="tabular" label="Glm - Group data on ${on_string}"/>
        <data name="year_var_group" from_work_dir="Output/mainglm_group/variationsAnnuellesGroupes_mainglm_group.tabular" format="tabular" label="Glm - Group yearly variations data on ${on_string}"/>
        <data name="glob_tend_group" from_work_dir="Output/mainglm_group/tendancesGlobalesGroupes_mainglm_group.tabular" format="tabular" label="Glm - Group tendencies on ${on_string}"/>
        <data name="plot_year_var_group" from_work_dir="Output/mainglm_group/variationsAnnuellesGroupes_mainglm_group.png" format="png" label="Glm - Group yearly variations plot on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="inputtabSpecies" value="tabSpecies.csv"/>
            <param name="input_y_var" value="mainglm_tab_years.tabular"/>
            <param name="input_glob_tendencies" value ="mainglm_tab_global.tabular"/>
            <param name="advanced" value="simple"/>
            <output name="data_group">
                <assert_contents>
                    <has_n_lines n="37"/>
                    <has_size value="3277" delta="100"/>
                </assert_contents>
            </output>
            <output name="year_var_group">
                <assert_contents>
                    <has_n_lines n="37"/>
                    <has_size value="1623" delta="100"/>
                </assert_contents>
            </output>
            <output name="glob_tend_group">
                <assert_contents>
                    <has_n_lines n="3"/>
                    <has_size value="154" delta="20"/>
                </assert_contents>
            </output>
            <output name="plot_year_var_group">
                <assert_contents>
                    <has_text text="PNG"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
=================================================
STOC Estimate species population variation
=================================================

**What it does**



Compute and plot trends of species population by specialization group, using a glm model. The same model than glm per species is used but results are aggregated by specialization group.


|

**Input description**

Two tabular files processed with the STOCs 'Preprocess population data' 'Filter species' on one hand and 'mainglm' tools on the other hand. 

One tabular species file, with a `species ID` column and species names.

|

**Output**


Two tabular files are created, they describe global tendencies and yearly variations per groups. One plot of yearly variations per group.
One tabular file describing species with several columns as species ID, species name, species scientific name and specialization status.
|

**Source**

UnPublished script available at http://www.vigienature.fr/sites/vigienature/files/atoms/files/analysestoceps_0.zip
the first version written by Romain Lorrilliere.

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