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comparison minimap2.xml @ 17:c0c2d0941de8 draft

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"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
comparison
equal deleted inserted replaced
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"