annotate pampa_macros.xml @ 0:3ab852a7ff53 draft

"planemo upload for repository https://github.com/ColineRoyaux/PAMPA-Galaxy commit 04381ca7162ec3ec68419e308194b91d11cacb04"

<macros>
    <token name="@VERSION@">0.0.2</token>
    <xml name="Pampa_requirements">
        <requirements>
            <requirement type="package" version="1.0.2">r-tidyr</requirement>
        </requirements>    
    </xml>
    <xml name="GLM_requirements">
        <requirements>
            <requirement type="package" version="1.2.2">r-gap</requirement>
            <requirement type="package" version="1.0.1">r-glmmtmb</requirement>
            <requirement type="package" version="1.4_13">r-multcomp</requirement>
            <requirement type="package" version="0.3.3.0">r-dharma</requirement>
        </requirements>    
    </xml>
    <xml name="Plot_requirements">
        <requirements>
            <requirement type="package" version="3.1.1">r-ggplot2</requirement>
            <requirement type="package" version="1.3_25">r-boot</requirement>
        </requirements>    
    </xml>
    <xml name="pampa_input_calculate">
        <param name="input" type="data" format="tabular" label="Input file" help="Observation data file, with location, year, species and abundance."/>
    </xml>
    <xml name="pampa_advanced_params_select">
        <param name="advanced" type="select" label="Specify advanced parameters">
            <option value="simple" selected="true">No, use program defaults.</option>
            <option value="advanced">Yes, see full parameter list.</option>
        </param>        
        <when value="simple">
        </when>        
    </xml>
    <xml name="pampa_advanced_params_select_GLM">
        <param name="advanced" type="select" label="Specify advanced parameters">
            <option value="simple" selected="true">No, use program defaults.</option>
            <option value="advanced">Yes, see full parameter list.</option>
        </param>        
        <when value="simple">
        </when>        
        <when value="advanced">
            <param name="distrib" type="select" label="Distribution for model">
                <option selected="true" value="None">Auto</option>
                <option value="gaussian">Gaussian</option>
                <option value="inverse.gaussian">Inverse Gaussian</option>
                <option value="poisson">Poisson</option>
                <option value="quasipoisson">Quasi-Poisson</option>
                <option value="binomial">Binomial</option>
                <option value="quasibinomial">Quasi-Binomial</option>
                <option value="Gamma">Gamma</option>
            </param>
            <param name="rdata" type="boolean" checked="yes" label="GLM object(s) as .Rdata output ?"/>
        </when>
    </xml>
    <xml name="pampa_input_GLM">
        <param name="input_metric" type="data" format="tabular" label="Input metrics file" help="Metrics data file, with location, year, and metrics informations that can be used as interest variable."/>
        <param name="input_unitobs" type="data" format="tabular" label="Unitobs informations file" help="Unitobs file, with all informations available about unitobs."/>
        <param name="varint" type="data_column" data_ref="input_metric" label="Interest variable from metrics file" help= "Choose the field of the interest variable."/>
    </xml>
    <xml name="pampa_var_GLM">
        <param name="varrep" type="select" label="Response variables" help= "Choose the response variables you want to include in your analysis." multiple="true">
            <option selected="true" value="year">Year</option>
            <option selected="true" value="site">Site</option>
            <option selected="true" value="habitat">Habitat</option>
        </param>
        <param name="varrand" type="select" label="Random effect ?" help="Allocate a random effect on site or year makes your model more reliable as random events on a peculiar site or year can affect populations, it takes account of pseudoreplication. However, avoid applying it on a less than 10 levels variable (less than 10 different sites and/or year)." multiple="true">
            <option value="year">Year</option>
            <option selected="true" value="site">Site</option>
        </param>
    </xml>
    <xml name="pampa_output_GLM">
        <data name="output_recap" from_work_dir="GLMSummaryFull.txt" format="txt" label="Simple statistics on chosen variables on ${on_string}"/>
        <data name="output_rate" from_work_dir="RatingGLM.txt" format="txt" label="Your analysis rating file on ${on_string}"/>
        <collection type="list" name="output_GLM">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.Rdata" visible="false" format="Rdata"/>
            <filter> settings['advanced'] == 'advanced' and settings['rdata']</filter>
        </collection>
    </xml>
    <xml name="pampa_bibref">
        <citations>
            <citation type="bibtex">
	    @unpublished{pampayves,
	    title={ PAMPA "ressources et biodiversité" scripts },
            author={Yves Reecht},
            url={https://wwz.ifremer.fr/pampa/Meth.-Outils/Outils}
            }
            </citation>
        </citations>
    </xml>
</macros>