Mercurial > repos > iuc > medaka_consensus_pipeline
comparison medaka_consensus.xml @ 14:cb34f00cc10f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 8051b858e0f5c6d7c1092754df02ed8303a53054
author | iuc |
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date | Mon, 27 Jun 2022 17:30:31 +0000 |
parents | 72b5e9dda577 |
children | 79e9a869f40e |
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13:72b5e9dda577 | 14:cb34f00cc10f |
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4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
7 <expand macro="version_command"/> | 7 <expand macro="version_command"/> |
8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
9 ln -s '$d' 'input_assembly.fa' && | 9 ## symlink seems insuffiencient (fai file is still created next to link target) |
10 cp '$d' 'input_assembly.fa' && | |
10 medaka_consensus | 11 medaka_consensus |
11 ## optional | 12 ## optional |
12 -m ${m} | 13 -m ${m} |
13 -b $b | 14 -b $b |
14 -o results | 15 -o results |
123 | 124 |
124 .. class:: infomark | 125 .. class:: infomark |
125 | 126 |
126 **Input** | 127 **Input** |
127 | 128 |
128 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. | 129 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. |
129 | 130 |
130 ---- | 131 ---- |
131 | 132 |
132 .. class:: infomark | 133 .. class:: infomark |
133 | 134 |