annotate venn.xml @ 0:36d4584a5ceb draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"

<tool id="ampvis2_venn" name="ampvis2 venn diagram" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="header"/>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$rscript'
    ]]></command>
    <configfiles>
        <configfile name="rscript"><![CDATA[
            library(ampvis2, quietly = TRUE)
            data <- readRDS("$data")
            plot <- amp_venn(
                data,
                #if $group_by
                    group_by = "$group_by",
                #end if
                cut_a = $cut_a,
                cut_f = $cut_f,
                text_size = $text_size,
                normalise = $normalise,
                ## detailed_output = TRUE seems not supported yet https://github.com/MadsAlbertsen/ampvis2/issues/132
                )
            ## names(plot)
            @OUTPUT_TOKEN@
        ]]></configfile>
    </configfiles>
    <inputs>
        <expand macro="rds_metadata_input_macro"/>
        <expand macro="metadata_select_discrete" argument="group_by" label="Group the data by" halp="Currently only supports a maximum of 3 different groups.">
            <validator type="expression" message="A maximum of 3 different groups is supported"><![CDATA[len(str(value).split(",")) < 4]]></validator>
        </expand>
        <param argument="cut_a" type="float" value="0.1" min="0" max="100" label="Abundance cutoff (percent)" help="OTU's below this abundance are excluded from the analysis"/>
        <param argument="cut_f" type="float" value="80" min="0" max="100" label="Frequency cutoff (percent)" help="OTU's within the top cut_f of the reads are considered a core OTU"/>
        <param argument="text_size" type="integer" value="5" min="1" label="Size of the plotted text."/>
        <expand macro="normalise_macro"/>
        <expand macro="out_format_macro"/>
    </inputs>
    <outputs>
        <expand macro="out_macro"/>
    </outputs>
    <tests>
        <!-- defaults -->
        <test expect_num_outputs="1">
            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
            <output name="plot" value="AalborgWWTPs-venn.pdf" ftype="pdf"/>
        </test>
        <!-- defaults + group_by -->
        <test expect_num_outputs="1">
            <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> 
            <param name="metadata_list" value="AalborgWWTPs-metadata.list"/> 
            <param name="group_by" value="Plant"/>
            <output name="plot" value="AalborgWWTPs-venn-group.pdf" ftype="pdf"/>
        </test>
    </tests>
    <help><![CDATA[
What it does
============

Calculates the number of "core" OTUs shared by groups given thresholds for how
frequent the OTUs should be above a certain abundance. Also returns the average
abundance of the OTUs in a particular group.

The Galaxy tool calls the `amp_venn
<https://madsalbertsen.github.io/ampvis2/reference/amp_venn.html>`_ function
of the ampvis2 package.

@HELP_RELATIVE_ABUNDANCES@

Input
=====

@HELP_RDS_INPUT@

@HELP_METADATA_LIST_INPUT@

Output
======

A venn diagram in the chosen output format.
    ]]></help>
    <expand macro="citations"/>
</tool>