annotate stoceps_macros.xml @ 1:e3e173ae01b0 draft

"planemo upload for repository https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc commit 5d749f3befe0a1f517c8af5f757e5b332d6374a2"

<macros>
    <token name="@VERSION@">0.0.1</token>
    <xml name="reshape_requirements">
        <requirements>
            <requirement type="package" version="0.8.8">r-reshape</requirement>
            <requirement type="package" version="1.12.0">r-data.table</requirement>
        </requirements>    
    </xml>
    <xml name="reshape2_requirements">
        <requirements>
            <requirement type="package" version="1.4.3">r-reshape2</requirement>
        </requirements>    
    </xml>
    <xml name="mainglm_requirements">
        <requirements>
            <requirement type="package" version="3.0.0">r-ggplot2</requirement>
            <requirement type="package" version="0.3_2">r-speedglm</requirement>
            <requirement type="package" version="1.10_1">r-arm</requirement>
            <requirement type="package" version="1.12.0">r-data.table</requirement>
            <requirement type="package" version="1.4.3">r-reshape2</requirement>
        </requirements>
    </xml>
    <xml name="temp_indic_requirements">
        <requirements>
            <requirement type="package" version="1.3_15">r-rodbc</requirement>
            <requirement type="package" version="0.8.8">r-reshape</requirement>
            <requirement type="package" version="1.12.0">r-data.table</requirement>
            <requirement type="package" version="1.4_3">r-rgdal</requirement>
            <requirement type="package" version="1.7.4">r-lubridate</requirement>
            <requirement type="package" version="4.6_2">r-doby</requirement>
            <requirement type="package" version="1.10_1">r-arm</requirement>
            <requirement type="package" version="3.1.0">r-ggplot2</requirement>
            <requirement type="package" version="1.0.0">r-scales</requirement>
            <requirement type="package" version="1.8_24">r-mgcv</requirement>
            <requirement type="package" version="1.8.4">r-plyr</requirement>
            <requirement type="package" version="0.3_2">r-speedglm</requirement>
            <requirement type="package" version="3.1_0">r-lmertest</requirement>
            <requirement type="package" version="0.2.3">r-glmmtmb</requirement>
        </requirements>
    </xml>
    <xml name="stoceps_input_filtered">
        <param name="input" type="data" format="tabular" label="Stoc filtered input" help="Input Stoc count file, shaped and filtered with the 'preprocess population data' and 'filter species' tools." />
    </xml>
    <xml name="stoceps_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="stoceps_compute_ic">
        <param name="compute_ic" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="yes" label="Compute confidence intervals"/>
    </xml>
    <xml name="stoceps_filter_glmmtmb">
        <filter> settings['advanced'] == 'advanced'</filter>
        <filter> settings['method'] == 'glmmtmb'</filter>
    </xml>
    <xml name="stoceps_filter_gam">
        <filter> settings['method'] == 'gam'</filter>
    </xml>
    <xml name="stoceps_bibref">
        <citations>
            <citation type="bibtex">
	    @unpublished{stocepsromain,
	    title={Vigie-Nature STOC unpublished scripts},
            author={Lorrilliere, R},
            url={http://www.vigienature.fr/sites/vigienature/files/atoms/files/analysestoceps_0.zip}
            }
            </citation>
        </citations>
    </xml>
</macros>