comparison macros.xml @ 3:afdfa35a89d9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 8533fe71d1d50f09348da2dc34941724407a1ffe"

2:c48d42d65d2b

            <requirement type="package" version="@DADA2_VERSION@">bioconductor-dada2</requirement>
            <yield/>
        </requirements>
    </xml>

    <token name="@DADA2_VERSION@">1.14</token>
    <token name="@WRAPPER_VERSION@">0</token>

    <xml name="version_command">
        <version_command><![CDATA[
echo $(R --version | grep version | grep -v GNU)", dada2 version" $(R --vanilla --slave -e "library(dada2); cat(sessionInfo()\$otherPkgs\$dada2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")

The intended use of the dada2 tools for paired sequencing data is shown in the following image.

.. image:: pairpipe.png

For single end data you the steps "Unzip collection" and "mergePairs" are not necessary.

More information may be found on the dada2 homepage:: https://benjjneb.github.io/dada2/index.html (in particular tutorials) or the documentation of dada2's R package https://bioconductor.org/packages/release/bioc/html/dada2.html (in particular the pdf which contains the full documentation of all parameters)
    ]]></token>
</macros>

3:afdfa35a89d9

            <requirement type="package" version="@DADA2_VERSION@">bioconductor-dada2</requirement>
            <yield/>
        </requirements>
    </xml>

    <token name="@DADA2_VERSION@">1.16</token>
    <token name="@WRAPPER_VERSION@">0</token>

    <xml name="version_command">
        <version_command><![CDATA[
echo $(R --version | grep version | grep -v GNU)", dada2 version" $(R --vanilla --slave -e "library(dada2); cat(sessionInfo()\$otherPkgs\$dada2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")

The intended use of the dada2 tools for paired sequencing data is shown in the following image.

.. image:: pairpipe.png

Note: In particular for the analysis of paired collections the collections should be sorted lexicographical
before the analysis.

For single end data you the steps "Unzip collection" and "mergePairs" are not necessary.

More information may be found on the dada2 homepage:: https://benjjneb.github.io/dada2/index.html (in particular tutorials) or the documentation of dada2's R package https://bioconductor.org/packages/release/bioc/html/dada2.html (in particular the pdf which contains the full documentation of all parameters)
    ]]></token>
</macros>