comparison macros.xml @ 3:0d30cb9b14cc draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6

2:7f712eb18230

<macros>
    <token name="@TOOL_VERSION@">2.7.22</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <token name="@PROFILE@">22.01</token>
    <xml name="header">
        <xrefs>
            <xref type="bio.tools">ampvis</xref>
        </xrefs>
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">r-ampvis2</requirement>
            <requirement type="package" version="2.1.1">r-readr</requirement>
        </requirements>
        <version_command><![CDATA[
echo $(R --version | grep "R version")", ampvis2 version" $(R --vanilla --slave -e "library(ampvis2, quietly = TRUE); sessionInfo()\$otherPkgs\$ampvis2\$Version" 2> /dev/null | grep -v -i "WARNING: ")
        ]]></version_command>

    </xml>

    <token name="@SAVE_TAX_LIST@"><![CDATA[
                for(level in colnames(data\$tax)){
                    for(u in unique(data\$tax[level])){
                        write(u, file="$taxonomy_list_out", append=T)
                    }
                }
    ]]></token>

    <token name="@SAVE_METADATA_LIST@"><![CDATA[

            </token>
            <yield/>
        </expand>
    </xml>

    <xml name="metadata_sample_select" token_argument="">
        <conditional name="@ARGUMENT@_cond">
            <param name="@ARGUMENT@_sel" type="select">
                <option value="no">No</option>
                <option value="variable">Metadata variable</option>
                <option value="sample">Specific sample</option>

            <when value="no"/>
            <when value="variable">
                <expand macro="metadata_select" argument="@ARGUMENT@" label="Metadata variable"/>
            </when>
            <when value="sample">
                <param argument="@ARGUMENT@" type="select" optional="true">
                    <options from_dataset="metadata_list">
                        <column name="name" index="1"/>
                        <column name="value" index="1"/>
                        <filter type="static_value" value="TRUE" column="2"/> <!-- filter samples -->
                        <filter type="unique_value" column="1"/>
                    </options>
                </param>
            </when>
        </conditional>
    </xml>

    <xml name="taxonomy_select_macro" token_argument="" token_optional="false" token_multiple="true">

3:0d30cb9b14cc

<macros>
    <token name="@TOOL_VERSION@">2.8.6</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">22.01</token>
    <xml name="header">
        <xrefs>
            <xref type="bio.tools">ampvis</xref>
        </xrefs>
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">r-ampvis2</requirement>
            <requirement type="package" version="2.1.5">r-readr</requirement>
            <requirement type="package" version="1.46.0">bioconductor-phyloseq</requirement>
        </requirements>
        <version_command><![CDATA[
echo $(R --version | grep "R version")", ampvis2 version" $(R --vanilla --slave -e "library(ampvis2, quietly = TRUE); sessionInfo()\$otherPkgs\$ampvis2\$Version" 2> /dev/null | grep -v -i "WARNING: ")
        ]]></version_command>

    </xml>

    <token name="@SAVE_TAX_LIST@"><![CDATA[
                for(level in colnames(data\$tax)){
                    for(u in unique(data\$tax[level])){
                        write(paste(u, level, sep="\t"), file="$taxonomy_list_out", append=T)
                    }
                }
    ]]></token>

    <token name="@SAVE_METADATA_LIST@"><![CDATA[

            </token>
            <yield/>
        </expand>
    </xml>

    <!-- metadata_sample_or_variable_select is currently unused (heatmap is documented to allow normalize by
         sample or variable, but only sample seems possible https://github.com/KasperSkytte/ampvis2/issues/168
         leaving it for now in case it can be fixed .. then metadata_sample_select could be removed) -->
    <xml name="metadata_sample_select" token_argument="">
        <param argument="@ARGUMENT@" type="select" optional="true">
            <options from_dataset="metadata_list">
                <column name="name" index="1"/>
                <column name="value" index="1"/>
                <filter type="static_value" value="TRUE" column="2"/> <!-- filter samples -->
                <filter type="unique_value" column="1"/>
            </options>
        </param>
    </xml>
    <xml name="metadata_sample_or_variable_select" token_argument="">
        <conditional name="@ARGUMENT@_cond">
            <param name="@ARGUMENT@_sel" type="select">
                <option value="no">No</option>
                <option value="variable">Metadata variable</option>
                <option value="sample">Specific sample</option>

            <when value="no"/>
            <when value="variable">
                <expand macro="metadata_select" argument="@ARGUMENT@" label="Metadata variable"/>
            </when>
            <when value="sample">
                <expand macro="metadata_sample_select"/>
            </when>
        </conditional>
    </xml>

    <xml name="taxonomy_select_macro" token_argument="" token_optional="false" token_multiple="true">