Mercurial > repos > iuc > medaka_consensus_pipeline
changeset 14:cb34f00cc10f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 8051b858e0f5c6d7c1092754df02ed8303a53054
| author | iuc |
|---|---|
| date | Mon, 27 Jun 2022 17:30:31 +0000 |
| parents | 72b5e9dda577 |
| children | 79e9a869f40e |
| files | macros.xml medaka_consensus.xml |
| diffstat | 2 files changed, 6 insertions(+), 5 deletions(-) [+] |
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--- a/macros.xml Thu Nov 18 20:01:28 2021 +0000 +++ b/macros.xml Mon Jun 27 17:30:31 2022 +0000 @@ -1,7 +1,7 @@ <macros> <token name="@TOOL_VERSION@">1.4.4</token> - <token name="@VERSION_SUFFIX@">0</token> - <token name="@PROFILE@">20.01</token> + <token name="@VERSION_SUFFIX@">1</token> + <token name="@PROFILE@">21.01</token> <xml name="bio_tools"> <xrefs> <xref type="bio.tools">medaka</xref> @@ -166,6 +166,6 @@ ]]></token> <token name="@REFERENCES@"><![CDATA[ -More information are available in the `manual <https://nanoporetech.github.io/medaka/index.html>`_ and `github <https://github.com/nanoporetech/medaka>`_. +More information are available in the `manual <https://github.com/nanoporetech/medaka/tree/master/docs>`_ and `github <https://github.com/nanoporetech/medaka>`_. ]]></token> </macros>
--- a/medaka_consensus.xml Thu Nov 18 20:01:28 2021 +0000 +++ b/medaka_consensus.xml Mon Jun 27 17:30:31 2022 +0000 @@ -6,7 +6,8 @@ <expand macro="requirements"/> <expand macro="version_command"/> <command detect_errors="exit_code"><![CDATA[ -ln -s '$d' 'input_assembly.fa' && +## symlink seems insuffiencient (fai file is still created next to link target) +cp '$d' 'input_assembly.fa' && medaka_consensus ## optional -m ${m} @@ -125,7 +126,7 @@ **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. +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. ----