Mercurial > repos > iuc > miniprot_index
changeset 0:bd3dc3b5aea5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot commit 931e98e27ac60b189e2dfbb1c99767bd17860c5e
| author | iuc |
|---|---|
| date | Mon, 19 Sep 2022 12:29:40 +0000 |
| parents | |
| children | d6a874226260 |
| files | macros.xml miniprot_index.xml test-data/input_genome.fasta.gz test-data/input_query.fasta.gz |
| diffstat | 4 files changed, 37 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Sep 19 12:29:40 2022 +0000 @@ -0,0 +1,3 @@ +<macros> + <token name="@TOOL_VERSION@">0.2</token> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/miniprot_index.xml Mon Sep 19 12:29:40 2022 +0000 @@ -0,0 +1,34 @@ +<tool id="miniprot_index" name="Miniprot index" version="@TOOL_VERSION@+galaxy0" profile="21.05"> + <description>build a genome index for miniprot</description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">miniprot</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + miniprot -d '$output_index' '$input_genome' + ]]></command> + <inputs> + <param name="input_genome" type="data" format="fasta,fasta.gz" label="Genomic sequence (FASTA)" help="Genomic contigs / scaffolds in FASTA format" /> + </inputs> + <outputs> + <!-- refine this when miniprot index format is in Galaxy datatypes --> + <data name="output_index" format="binary" label="Miniprot index on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="input_genome" value="input_genome.fasta.gz" ftype="fasta" /> + <output name="output_index" ftype="binary"> + <assert_contents> + <has_size value="135707709" delta="1000" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + Pre-index genomic sequences (contigs, scaffolds or chromosomes) for use in the miniprot_ protein to genome alignment tool. + + .. _miniprot: https://github.com/lh3/miniprot + ]]></help> +</tool> \ No newline at end of file