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comparison stacks_populations.xml @ 11:95286af4139b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 5f2ec13ecca435abaac2b99ba21f1d6497ec7139"
author iuc
date Tue, 22 Mar 2022 23:19:46 +0000
parents d504d945a655
children d1fad35bdb4a
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10:d504d945a655 11:95286af4139b
1 <tool id="stacks_populations" name="Stacks: populations" version="@WRAPPER_VERSION@.1"> 1 <tool id="stacks_populations" name="Stacks: populations" version="@WRAPPER_VERSION@.2">
2 <description>analyze a population of individual samples ('populations' program)</description> 2 <description>analyze a population of individual samples ('populations' program)</description>
3 <expand macro="bio_tools"/>
3 <macros> 4 <macros>
4 <import>macros.xml</import> 5 <import>macros.xml</import>
5 </macros> 6 </macros>
6 <expand macro="requirements"/> 7 <expand macro="requirements"/>
7 <expand macro="stdio"/> 8 <expand macro="stdio"/>
65 ## Fstats 66 ## Fstats
66 $fstats 67 $fstats
67 68
68 #if $options_kernel.kernel 69 #if $options_kernel.kernel
69 -k 70 -k
70 --window_size $options_kernel.window 71 --sigma $options_kernel.sigma
71 #end if 72 #end if
72 73
73 ## Bootstrap resampling options 74 ## Bootstrap resampling options
74 #if $bootstrap_resampling.bootstrap_resampling_mode.bootstrap_all 75 #if $bootstrap_resampling.bootstrap_resampling_mode.bootstrap_all
75 --bootstrap 76 --bootstrap
211 <param name="fstats" argument="--fstats" truevalue="--fstats" falsevalue="" type="boolean" checked="false" label="Enable SNP and haplotype-based F statistics" /> 212 <param name="fstats" argument="--fstats" truevalue="--fstats" falsevalue="" type="boolean" checked="false" label="Enable SNP and haplotype-based F statistics" />
212 213
213 <conditional name="options_kernel"> 214 <conditional name="options_kernel">
214 <param name="kernel" type="boolean" checked="false" truevalue="-k" falsevalue="" label="enable kernel-smoothed FIS, π, and FST calculations" /> 215 <param name="kernel" type="boolean" checked="false" truevalue="-k" falsevalue="" label="enable kernel-smoothed FIS, π, and FST calculations" />
215 <when value="-k"> 216 <when value="-k">
216 <param name="window" type="integer" value="150" label="window size" help="distance over which to average values (sigma, default 150Kb)" /> 217 <param name="sigma" type="integer" value="150" label="Sigma" help="Standard deviation of the kernel smoothing weight distribution (sigma, default 150Kb)" />
217 </when> 218 </when>
218 <when value=""> 219 <when value="">
219 </when> 220 </when>
220 </conditional> 221 </conditional>
221 222
438 indv_06 2 439 indv_06 2
439 440
440 441
441 **Output files** 442 **Output files**
442 443
443 - XXX.tags.tsv file:: 444 - XXX.tags.tsv file:
444 445
445 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ 446 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
446 447
447 Notes: For the tags file, each stack will start in the file with a consensus sequence for the entire stack followed by the flags for that stack. Then, each individual read that was merged into that stack will follow. The next stack will start with another consensus sequence. 448 Notes: For the tags file, each stack will start in the file with a consensus sequence for the entire stack followed by the flags for that stack. Then, each individual read that was merged into that stack will follow. The next stack will start with another consensus sequence.
448 449
449 450
450 - XXX.snps.tsv file:: 451 - XXX.snps.tsv file:
451 452
452 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ 453 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
453 454
454 Notes: If a stack has two SNPs called within it, then there will be two lines in this file listing each one. 455 Notes: If a stack has two SNPs called within it, then there will be two lines in this file listing each one.
455 456
456 457
457 - XXX.alleles.tsv file:: 458 - XXX.alleles.tsv file:
458 459
459 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ 460 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
460 461
461 462
462 - XXX.matches.tsv file:: 463 - XXX.matches.tsv file:
463 464
464 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ 465 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_
465 466
466 Notes: Each line in this file records a match between a catalog locus and a locus in an individual, for a particular haplotype. The Batch ID plus the Catalog ID together represent a unique locus in the entire population, while the Sample ID and the Stack ID together represent a unique locus in an individual sample. 467 Notes: Each line in this file records a match between a catalog locus and a locus in an individual, for a particular haplotype. The Batch ID plus the Catalog ID together represent a unique locus in the entire population, while the Sample ID and the Stack ID together represent a unique locus in an individual sample.
467 468