annotate merge_ampvis2.xml @ 7:378ce300fb3d draft default tip

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

<tool id="ampvis2_merge_ampvis2" name="ampvis2 merge ampvis2 data sets" 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)
            merged <- amp_merge_ampvis2(
            #for d in $data
                readRDS("$d"), 
            #end for
            by_refseq = $by_refseq
            )
            saveRDS(merged, "$output")
            merged
        ]]></configfile>
    </configfiles>
    <inputs>
        <expand macro="rds_input_macro" multiple="true"/>
        <param argument="by_refseq" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Merge by exact matches between DNA reference sequences" help="The full DNA sequences will then be used as the new names in the output."/>
        <!--  TODO refseq_names = NULL, rename_unmatched = TRUE, unmatched_prefix = "unmatched" -->
    </inputs>
    <outputs>
        <data name="output" format="ampvis2"/>
    </outputs>
    <tests>
        <!-- defaults -->
        <test expect_num_outputs="1">
            <param name="data" value="AalborgWWTPs.2010.rds,AalborgWWTPs.2011.rds" ftype="ampvis2"/> 
            <output name="output" ftype="ampvis2">
                <assert_contents>
                    <has_size value="70888" delta="1000"/>
                </assert_contents>
            </output>
            <assert_stdout>
                <!--check that the merged data has 13 samples-->
                <has_text text="13          125         6714          193         1019          475"/>
            </assert_stdout>
        </test>
    </tests>
    <help><![CDATA[
What it does
============

Merge any number of ampvis2 data sets into a single data set.

The Galaxy tool calls the `amp_merge_ampvis2
<https://kasperskytte.github.io/ampvis2/reference/amp_merge_ampvis2.html>`_ function
of the ampvis2 package.

Input
=====

@HELP_RDS_INPUT@

Details
=======

It's important to ensure that the taxonomy for all OTU's across data sets is
generated in the exact same way with the same database. When **Merge by exact matches between DNA reference sequences** is not checked
it's likewise important to ensure that OTU ID's are not arbitrary between data
sets and that they are corresponding to the same sequences across data sets
(objects). When **Merge by exact matches between DNA reference sequences** is checked the full DNA sequences will be used as the new
OTU ID's. 

Currently, phylogenetic trees are not merged.

Output
======

The merged data set
    ]]></help>
    <expand macro="citations"/>
</tool>