comparison heatmap.xml @ 2:b95c7b3f411e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9fe04d29ea604a152144908dbd20c0754695a025

1:cdc3f2941bdf

<tool id="ampvis2_heatmap" name="ampvis2 heatmap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="header"/>

                    normalise_by = "$normalise_by",
                #end if
                #if $scale_by
                    scale_by = "$scale_by",
                #end if
                ## color_vector = NULL
                ## round = 1,
                #if $output_options.out_format == "tabular"
                    textmap = TRUE,
                #else
                    textmap = FALSE,

                        <filter type="unique_value" column="1"/>
                    </options>
                </param>
            </when>
        </conditional>
        <!-- https://github.com/KasperSkytte/ampvis2/issues/168 
            if this is possible again reuse: metadata_sample_or_variable_select ? -->
        <expand macro="metadata_sample_select" argument="normalise_by" label="Normalize counts by a variable or a specific sample"/>
        <expand macro="metadata_select_discrete" argument="scale_by" label="Scale the abundances by a variable in the metadata"/>

                <param name="function_data" value="AalborgWWTPs-functions.tsv" ftype="tsv"/>
                <param name="functions" value="Foo,Bar"/>
            </conditional>
            <output name="plot" value="AalborgWWTPs-heatmap-plot_foo_file.pdf" ftype="pdf" compare="sim_size"/>
        </test>
    
    </tests>
    <help><![CDATA[
What it does
============

2:b95c7b3f411e

<tool id="ampvis2_heatmap" name="ampvis2 heatmap" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@" license="MIT">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="header"/>

                    normalise_by = "$normalise_by",
                #end if
                #if $scale_by
                    scale_by = "$scale_by",
                #end if
                 color_vector = c("$color_palette_start", "$color_palette_end"),
                ## round = 1,
                #if $output_options.out_format == "tabular"
                    textmap = TRUE,
                #else
                    textmap = FALSE,

                        <filter type="unique_value" column="1"/>
                    </options>
                </param>
            </when>
        </conditional>
        <param argument="color_palette_start" type="color" label="Start color for the heatmap" help="Choose the start color for the heatmap."/>
        <param argument="color_palette_end" type="color" label="End color for the heatmap" help="Choose the end color for the heatmap."/>
        <!-- https://github.com/KasperSkytte/ampvis2/issues/168 
            if this is possible again reuse: metadata_sample_or_variable_select ? -->
        <expand macro="metadata_sample_select" argument="normalise_by" label="Normalize counts by a variable or a specific sample"/>
        <expand macro="metadata_select_discrete" argument="scale_by" label="Scale the abundances by a variable in the metadata"/>

                <param name="function_data" value="AalborgWWTPs-functions.tsv" ftype="tsv"/>
                <param name="functions" value="Foo,Bar"/>
            </conditional>
            <output name="plot" value="AalborgWWTPs-heatmap-plot_foo_file.pdf" ftype="pdf" compare="sim_size"/>
        </test>
        <!-- test with different color palettes -->
        <test expect_num_outputs="1">
            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
            <param name="color_palette_start" value="red"/>
            <param name="color_palette_end" value="yellow"/>
            <output name="plot" value="AalborgWWTPs-heatmap-red-yellow.pdf" ftype="pdf" compare="sim_size"/>
        </test>
        <test expect_num_outputs="1">
            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
            <param name="color_palette_start" value="blue"/>
            <param name="color_palette_end" value="green"/>
            <output name="plot" value="AalborgWWTPs-heatmap-blue-green.pdf" ftype="pdf" compare="sim_size"/>
        </test>
    
    </tests>
    <help><![CDATA[
What it does
============