Mercurial > repos > dfornika > medaka_consensus
changeset 0:eecb8c891134 draft
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"
| author | dfornika |
|---|---|
| date | Wed, 11 Mar 2020 00:48:06 +0000 |
| parents | |
| children | 2bcf9108d73c |
| files | medaka_consensus.xml test-data/res.hdf test-data/res.primertrimmed.sorted.bam test-data/res.primertrimmed.sorted.bam.bai |
| diffstat | 4 files changed, 48 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/medaka_consensus.xml Wed Mar 11 00:48:06 2020 +0000 @@ -0,0 +1,48 @@ +<tool id="medaka_consensus" name="medaka_consensus" version="@VERSION@" profile="19.01"> + <description>Creates a consensus sequence from an alignment generated from nanopore sequence data</description> + <macros> + <token name="@VERSION@">0.11.5</token> + </macros> + <requirements> + <requirement type="package" version="@VERSION@">medaka</requirement> + <requirement type="package" version="1.9">samtools</requirement> + </requirements> + <version_command>medaka --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + ln -s '${input_alignment}' alignment.bam && + samtools index alignment.bam && + medaka consensus + --threads \${GALAXY_SLOTS:-4} + --model '${model}' + alignment.bam + '${consensus_hdf}' + > '${log}' + ]]></command> + <inputs> + <param name="input_alignment" type="data" format="bam" label="Input Alignment"/> + <param name="model" type="select" label="Model"> + <option value="r941_min_fast_g303">r941_min_fast_g303</option> + <option value="r941_min_high_g303" selected="True">r941_min_high_g303</option> + <option value="r941_min_high_g330">r941_min_high_g330</option> + <option value="r941_min_high_g344">r941_min_high_g344</option> + <option value="r941_prom_fast_g303">r941_prom_fast_g303</option> + <option value="r941_prom_high_g303">r941_prom_high_g303</option> + <option value="r941_prom_high_g344">r941_prom_high_g344</option> + <option value="r941_prom_high_g330">r941_prom_high_g330</option> + <option value="r10_min_high_g303">r10_min_high_g303</option> + <option value="r10_min_high_g340">r10_min_high_g340</option> + <option value="r103_min_high_g345">r103_min_high_g345</option> + <option value="r941_prom_snp_g303">r941_prom_snp_g303</option> + <option value="r941_prom_variant_g303">r941_prom_variant_g303</option> + <option value="r941_min_high_g340_rle">r941_min_high_g340_rle</option> + </param> + </inputs> + <outputs> + <data name="consensus_hdf" format="binary" label="${tool.name} on ${on_string}: consensus hdf" /> + <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="log.txt"/> + </outputs> + <tests> + </tests> + <help><![CDATA[ + ]]></help> +</tool>