Mercurial > repos > fubar > mashmap
changeset 10:08a74c1a4562 draft default tip
planemo upload
| author | fubar |
|---|---|
| date | Sat, 24 Feb 2024 08:29:59 +0000 |
| parents | dc53eb4354a6 |
| children | |
| files | mashmap.xml |
| diffstat | 1 files changed, 6 insertions(+), 6 deletions(-) [+] |
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--- a/mashmap.xml Sat Feb 24 08:20:07 2024 +0000 +++ b/mashmap.xml Sat Feb 24 08:29:59 2024 +0000 @@ -1,6 +1,6 @@ <tool name="mashmap" id="mashmap" version="1.19.2" profile="22.05"> <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay--> - <!--Created by toolfactory@galaxy.org at 24/02/2024 19:18:09 using the Galaxy Tool Factory.--> + <!--Created by toolfactory@galaxy.org at 24/02/2024 19:28:59 using the Galaxy Tool Factory.--> <description>Fast local alignment boundaries</description> <requirements> <requirement version="3.1.3" type="package">mashmap</requirement> @@ -24,6 +24,9 @@ #if int($sketchSize) > 0: -J '$sketchSize' \ #end if +#if $dense: +--dense \ +#end if #if len($reflist) == 1: -r '$reflist' -q 'query' && #else @@ -37,10 +40,7 @@ <param name="perc_identity" type="float" value="85.0" label="Identity threshold" help="By default, it is set to 85, implying mappings with 85 or more identity should be reported. For example, it can be set to 80to account for more noisy long-read datasets or 95 for mapping human genome assembly to human reference."/> <param name="seqLength" type="integer" value="5000" label="Minimum segment length" help="Default is 5,000 bp. Sequences below this length are ignored. Mashmap provides guarantees on reporting local alignments of length twice this value."/> <param name="sketchSize" type="integer" value="0" label="Sketch size - leave 0 for automatic setting based" help="This parameter sets the seed density of the winnowing scheme, gauranteeing that the minhash will be calculated from a sample of sketchSize k-mers for each segment. It is set automatically based on --pi but can be manually set as well."/> - <param name="dense" type="select" label="Dense sketching" help="This flag will increase the seed density substantially, resulting in a density of roughly 0.02 * (1 + (1 - pi) / .05) where pi is the perc_identity threshold. This leads to longer runtimes and higher RAM usage, but significantly more accurate estimates of ANI."> - <option value="">No dense sketching</option> - <option value="--dense">Dense sketching</option> - </param> + <param name="dense" type="boolean" value="false" label="Dense sketching" help="This flag will increase the seed density substantially, resulting in a density of roughly 0.02 * (1 + (1 - pi) / .05) where pi is the perc_identity threshold. This leads to longer runtimes and higher RAM usage, but significantly more accurate estimates of ANI." checked="false" truevalue="--dense" falsevalue=""/> <param name="filtermode" type="select" label="Filter mode" help="Mashmap implements a plane-sweep based algorithm to perform the alignment filtering. Similar to delta-filter in nucmer, different filtering options are provided that are suitable for long read or assembly mapping. Option -f map is suitable for reporting the best mappings for long reads, whereas -f one-to-one is suitable for reporting orthologous mappings among all computed assembly to genome mappings."> <option value="map">map - best mapping for long reads</option> <option value="one-to-one">one-to-one - best for mapping orthologous reads</option> @@ -58,7 +58,7 @@ <param name="perc_identity" value="85.0"/> <param name="seqLength" value="5000"/> <param name="sketchSize" value="0"/> - <param name="dense" value=""/> + <param name="dense" value="false"/> <param name="filtermode" value="map"/> </test> </tests>