Mercurial > repos > thanhlv > medaka
changeset 0:c830020a14e9 draft default tip
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/medaka commit dad2b95d9266fd996ef130e844f43c5d0e686e43-dirty
| author | thanhlv |
|---|---|
| date | Fri, 20 Sep 2019 05:40:32 -0400 |
| parents | |
| children | |
| files | medaka.xml |
| diffstat | 1 files changed, 46 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/medaka.xml Fri Sep 20 05:40:32 2019 -0400 @@ -0,0 +1,46 @@ +<tool id="medaka" name="medaka" version="@VERSION@"> + <description> creates a consensus sequence from nanopore sequencing data</description> + <macros> + <token name="@VERSION@">0.9.1</token> + </macros> + <requirements> + <requirement type="package" version="@VERSION@">medaka</requirement> + </requirements> + <version_command>medaka --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + medaka_consensus + -i ${basecalled} + -d ${draft} + -o out_dir + -t \${GALAXY_SLOTS:-4} + -m '${model}' + ]]> </command> + + <inputs> + <param name="basecalled" type="data" format="fastq,fastq.gz,fasta.fasta.gz" label="Basecalled data"/> + <param name="model" type="select" label="Model"> + <option value="r941_min_fast">r941_min Fast</option> + <option value="r941_min_high" selected="True">r941_min High Accuracy</option> + <option value="r941_prom_fast">r941_prom_fast</option> + <option value="r941_prom_high">r941_prom_high</option> + <option value="r10_min_high">r10_min_high</option> + </param> +<<<<<<< HEAD + <param name="draft" type="data" format="fasta,fasta.gz" label="Draft assemblies" help="The input assembly should be +======= + <param name="draft" type="data" format="fasta.fasta.gz" label="Draft assemblies" help="The input assembly should be +>>>>>>> c89b7c7b0cc586ca9177e02deffae21a4fd3969e +preprocessed with racon"/> + </inputs> + + <outputs> + <collection name="list_output" type="list" label="Output"> + <discover_datasets pattern="__name_and_ext__" directory="out_dir"/> + </collection> + </outputs> + <help><![CDATA[ + ]]> </help> + <citations> + <citation type="doi">10.1186/1471-2105-12-385</citation> + </citations> +</tool>