Mercurial > repos > iuc > minimap2
comparison minimap2.xml @ 17:c0c2d0941de8 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minimap2 commit b5d3813c1e592400682b7c68ebb8c240f8e86bb4"
| author | iuc |
|---|---|
| date | Fri, 19 Nov 2021 14:35:04 +0000 |
| parents | 7db8d4bc1eea |
| children | 92678fcb1a5f |
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| 16:6b1e195506a3 | 17:c0c2d0941de8 |
|---|---|
| 45 -f $mapping_options.f | 45 -f $mapping_options.f |
| 46 #end if | 46 #end if |
| 47 #if str($mapping_options.min_occ_floor): | 47 #if str($mapping_options.min_occ_floor): |
| 48 --min-occ-floor $mapping_options.min_occ_floor | 48 --min-occ-floor $mapping_options.min_occ_floor |
| 49 #end if | 49 #end if |
| 50 --q-occ-frac $mapping_options.q_occ_frac | |
| 50 #if str($mapping_options.g): | 51 #if str($mapping_options.g): |
| 51 -g $mapping_options.g | 52 -g $mapping_options.g |
| 52 #end if | 53 #end if |
| 53 #if str($mapping_options.r): | 54 #if str($mapping_options.r): |
| 54 -r $mapping_options.r | 55 -r $mapping_options.r |
| 257 <param name="upper_limit" type="integer" min="0" max="10000" value="" label="K-mer ocurrence upper limit"/> | 258 <param name="upper_limit" type="integer" min="0" max="10000" value="" label="K-mer ocurrence upper limit"/> |
| 258 </when> | 259 </when> |
| 259 <when value=""> | 260 <when value=""> |
| 260 </when> | 261 </when> |
| 261 </conditional> | 262 </conditional> |
| 262 <param argument="--min-occ-floor" name="min_occ_floor" type="integer" label="Force minimap2 to always use k-mers occuring this many times or fewer" help="Maximum occurence is the number of repetitive minimizers determined by '-f' or this value, whichever is higher." optional="true" /> | 263 <param argument="--min-occ-floor" type="integer" label="Force minimap2 to always use k-mers occuring this many times or fewer" help="Maximum occurence is the number of repetitive minimizers determined by '-f' or this value, whichever is higher." optional="true" /> |
| 264 <param argument="--q-occ-frac" type="float" value="0.01" label="Discard a query minimizer" | |
| 265 help="Discard a query minimizer if its occurrence is higher than this fraction of query minimizers and than the reference occurrence threshold. It allows to avoid extremely long mapping time for pathologic reads with highly repeated k-mers not in the reference. Set to 0 to disable the new heuristic." /> | |
| 266 | |
| 263 <param argument="-g" type="integer" value="" optional="true" label="Stop chain enlongation if there are no minimizers in INT-bp" help="default=5000"/> | 267 <param argument="-g" type="integer" value="" optional="true" label="Stop chain enlongation if there are no minimizers in INT-bp" help="default=5000"/> |
| 264 <param argument="-r" type="integer" value="" optional="true" label="Bandwidth used in chaining and DP-based alignment" help="default=500" /> | 268 <param argument="-r" type="integer" value="" optional="true" label="Bandwidth used in chaining and DP-based alignment" help="default=500" /> |
| 265 <param argument="-n" type="integer" value="" optional="true" label="Minimal number of minimizers on a chain" help="default=3"/> | 269 <param argument="-n" type="integer" value="" optional="true" label="Minimal number of minimizers on a chain" help="default=3"/> |
| 266 <param argument="-m" type="integer" value="" optional="true" label="Minimal chaining score (matching bases minus log gap penalty)" help="default=40"/> | 270 <param argument="-m" type="integer" value="" optional="true" label="Minimal chaining score (matching bases minus log gap penalty)" help="default=40"/> |
| 267 <param argument="--max-chain-skip" type="integer" value="" optional="true" | 271 <param argument="--max-chain-skip" type="integer" value="" optional="true" |