comparison medaka_consensus.xml @ 14:cb34f00cc10f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 8051b858e0f5c6d7c1092754df02ed8303a53054

13:72b5e9dda577

        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
ln -s '$d' 'input_assembly.fa' &&
medaka_consensus
## optional
-m ${m}
-b $b
-o results

.. class:: infomark

**Input**

An *assembly* in .fasta format and *basecalls* in .fasta or .fastq format are required. See `Creating a Draft Assembly  <https://nanoporetech.github.io/medaka/walkthrough.html#basecalling-and-draft-assembly>`_ for a detailed example of one method of obtaining these.

----

.. class:: infomark

14:cb34f00cc10f

        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
## symlink seems insuffiencient (fai file is still created next to link target)
cp '$d' 'input_assembly.fa' &&
medaka_consensus
## optional
-m ${m}
-b $b
-o results

.. class:: infomark

**Input**

An *assembly* in .fasta format and *basecalls* in .fasta or .fastq format are required. See `Creating a Draft Assembly  <https://github.com/nanoporetech/medaka/blob/master/docs/walkthrough.rst>`_ for a detailed example of one method of obtaining these.

----

.. class:: infomark