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comparison macros.xml @ 5:226949352e31 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit a1c079107b72dc08612fa664897bb9d627624e52-dirty
author jjohnson
date Wed, 27 Nov 2019 12:11:14 -0500
parents aaeb63501369
children
comparison
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4:aaeb63501369 5:226949352e31
282 <action name="comment_lines" type="metadata" default="4" /> 282 <action name="comment_lines" type="metadata" default="4" />
283 <action name="column_names" type="metadata" default="rank,clade,number of ${sum_titles}" /> 283 <action name="column_names" type="metadata" default="rank,clade,number of ${sum_titles}" />
284 </actions> 284 </actions>
285 </data> 285 </data>
286 </xml> 286 </xml>
287 <token name="@OPTIONS_HELP@"><![CDATA[
288
289 Optional arguments:
290 -r, --range cut-off range after alignment [0-49] (default: 10).
291 -f, --fraction fraction of bit-score support for each classification
292 [0-0.99] (default: 0.5).
293 -p, --proteins_fasta
294 Path to predicted proteins fasta file. If supplied,
295 CAT will skip the protein prediction step.
296 -a, --diamond_alignment
297 Path to DIAMOND alignment table. If supplied, CAT will
298 skip the DIAMOND alignment step and directly classify
299 the sequences. A predicted proteins fasta file should
300 also be supplied with argument [-p / --proteins].
301
302
303 DIAMOND specific optional arguments:
304 --sensitive Run DIAMOND in sensitive mode (default: not enabled).
305
306 --block_size DIAMOND block-size parameter (default: 2.0). Lower
307 numbers will decrease memory and temporary disk space
308 usage.
309
310 --index_chunks
311 DIAMOND index-chunks parameter (default: 4). Set to 1
312 on high memory machines. The parameter has no effect
313 on temporary disk space usage.
314
315 --top
316 DIAMOND top parameter [0-50] (default: 50). Governs
317 hits within range of best hit that are written to the
318 alignment file. This is not the [-r / --range]
319 parameter!
320
321
322 Setting the DIAMOND --top parameter
323
324 You can speed up DIAMOND considerably, and at the same time greatly reduce disk usage, by setting the DIAMOND --top parameter to lower values. This will govern hits within range of the best hit that are written to the alignment file.
325
326 You have to be very carefull to 1) not confuse this parameter with the r / --range parameter, which does a similar cut-off but after alignment and 2) be aware that if you want to run CAT or BAT again afterwards with different values of the -r / --range parameter, your options will be limited to the range you have chosen with --top earlier, because all hits that fall outside this range will not be included in the alignment file. Importantly, CAT and BAT currently do not warn you if you choose -r / --range in a second run higher than --top in a previous one, so it's up to you to remember this!
327
328 If you have understood all this, or you do not plan to tune -r / --range at all afterwards, you can enjoy a huge speedup with much smaller alignment files! For CAT you can for example set --top 11 and for BAT --top 6.
329
330 ]]></token>
287 <token name="@COMMON_HELP@"><![CDATA[ 331 <token name="@COMMON_HELP@"><![CDATA[
288 The CAT/BAT workflow is described at: https://github.com/dutilh/CAT 332 The CAT/BAT workflow is described at: https://github.com/dutilh/CAT
289 ]]></token> 333 ]]></token>
290 <xml name="citations"> 334 <xml name="citations">
291 <citations> 335 <citations>