Mercurial > repos > dfornika > unicycler
changeset 1:2f02b1585757 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 9aca1f5531db1e71338919c63a4093c0b1e0cfd5-dirty
| author | dfornika |
|---|---|
| date | Fri, 04 Oct 2019 17:34:14 -0400 |
| parents | a2fa4a2588bc |
| children | |
| files | unicycler.xml |
| diffstat | 1 files changed, 6 insertions(+), 1 deletions(-) [+] |
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--- a/unicycler.xml Mon Sep 23 20:04:43 2019 -0400 +++ b/unicycler.xml Fri Oct 04 17:34:14 2019 -0400 @@ -88,6 +88,9 @@ #end if --kmer_count '$spades.kmer_count' --depth_filter '$spades.depth_filter' +#if $graph_clean.largest_component + --largest_component +#end if ## Rotation Options section ## ---------------------------------------------------------- $rotation.no_rotate @@ -163,6 +166,8 @@ <param argument="--kmer_count" type="integer" min="0" value="10" label="Number of k-mer steps to use in SPAdes assembly"/> <param argument="--depth_filter" type="float" min="0" max="1" value="0.25" label="Filter out contigs lower than this fraction of the chromosomal depth" help="It is done if does not result in graph dead ends"/> + <param argument="--largest_component" type="boolean" checked="false" + label="Only keep the largest connected component of the assembly graph"/> </section> <section name="rotation" expanded="false" title="Rotation options" help="These options control the rotation of completed circular sequence near the end of the Unicycler pipeline. Use this ONLY if you know what you are doing!"> @@ -182,7 +187,7 @@ <param argument="--min_component_size" type="integer" min="0" value="1000" label="Unbridged graph components smaller than this size will be removed from the final graph" /> <param argument="--min_dead_end_size" type="integer" min="0" value="1000" - label="Graph dead ends smaller than this size will be removed from the final graph"/> + label="Graph dead ends smaller than this size will be removed from the final graph"/> </section> <section name="lr_align" expanded="false" title="Long read alignment parameters" help="These options control the alignment of long reads to the assembly graph."> <param argument="--contamination" optional="true" type="data" format="fasta"