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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
author iuc
date Wed, 17 Oct 2018 11:41:46 -0400
parents f041f5a855cc
children edc5004afbaf
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1:f041f5a855cc 2:b2fbfb61f019
1 <tool id="iqtree" name="IQ-TREE" version="1.5.5.1" > 1 <tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@.1" >
2 <description>Phylogenomic / evolutionary tree construction from multiple sequences</description> 2 <description>Phylogenomic / evolutionary tree construction from multiple sequences</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="1.5.5">iqtree</requirement> 4 <import>iqtree_macros.xml</import>
5 </requirements> 5 </macros>
6 <expand macro="requirements" />
6 <command detect_errors='exit_code' ><![CDATA[ 7 <command detect_errors='exit_code' ><![CDATA[
7 iqtree 8 iqtree
8 -pre PREF 9 -pre PREF
9 -nt \${GALAXY_SLOTS:-10} 10 -nt \${GALAXY_SLOTS:-10}
10 -redo 11 -redo
360 </param> 361 </param>
361 </when> 362 </when>
362 </conditional> 363 </conditional>
363 <param argument="-rcluster" type="integer" optional="true" label="Specify the percentage for the relaxed clustering algorithm (Lanfear et al., 2014)" help="This is similar to --rcluster-percent option of PartitionFinder. For example, with -rcluster 10 only the top 10% partition schemes are considered to save computations." /> 364 <param argument="-rcluster" type="integer" optional="true" label="Specify the percentage for the relaxed clustering algorithm (Lanfear et al., 2014)" help="This is similar to --rcluster-percent option of PartitionFinder. For example, with -rcluster 10 only the top 10% partition schemes are considered to save computations." />
364 <param argument="-mset" type="text" optional="true" label="Specify the name of a program (raxml, phyml or mrbayes) to restrict to only those models supported by the specified program" help="Alternatively, one can specify a comma-separated list of base models. For example, -mset WAG,LG,JTT will restrict model selection to WAG, LG, and JTT instead of all 18 AA models to save computations."> 365 <param argument="-mset" type="text" optional="true" label="Specify the name of a program (raxml, phyml or mrbayes) to restrict to only those models supported by the specified program" help="Alternatively, one can specify a comma-separated list of base models. For example, -mset WAG,LG,JTT will restrict model selection to WAG, LG, and JTT instead of all 18 AA models to save computations.">
365 <sanitizer> 366 <expand macro="sanitize_query"
366 <valid initial="string.ascii_uppercase,string.punctuation" /> 367 validinitial="string.ascii_uppercase,string.punctuation" />
367 </sanitizer>
368 </param> 368 </param>
369 <param argument="-msub" type="select" label="Specify either nuclear, mitochondrial, chloroplast or viral to restrict to those AA models designed for specified source." help=""> 369 <param argument="-msub" type="select" label="Specify either nuclear, mitochondrial, chloroplast or viral to restrict to those AA models designed for specified source." help="">
370 <option value="nuclear">nuclear</option> 370 <option value="nuclear">nuclear</option>
371 <option value="mitochondrial">mitochondrial</option> 371 <option value="mitochondrial">mitochondrial</option>
372 <option value="chloroplast">chloroplast</option> 372 <option value="chloroplast">chloroplast</option>
373 <option value="viral">viral</option> 373 <option value="viral">viral</option>
374 </param> 374 </param>
375 <param argument="-mfreq" type="text" optional="true" label="Specify a comma-separated list of frequency types for model selection" > 375 <param argument="-mfreq" type="text" optional="true" label="Specify a comma-separated list of frequency types for model selection" >
376 <sanitizer> 376 <expand macro="sanitize_query"
377 <valid initial="string.ascii_uppercase,string.digits,x,string.punctuation" /> 377 validinitial="string.ascii_uppercase,string.digits,x,string.punctuation" />
378 </sanitizer>
379 </param> 378 </param>
380 <param argument="-mrate" type="text" optional="true" label="Specify a comma-separated list of rate heterogeneity types for model selection"> 379 <param argument="-mrate" type="text" optional="true" label="Specify a comma-separated list of rate heterogeneity types for model selection">
381 <sanitizer> 380 <expand macro="sanitize_query"
382 <valid initial="string.ascii_uppercase,string.punctuation" /> 381 validinitial="string.ascii_uppercase,string.punctuation" />
383 </sanitizer>
384 </param> 382 </param>
385 <param argument="-cmin" type="integer" value="2" optional="true" label="Specify minimum number of categories for FreeRate model"/> 383 <param argument="-cmin" type="integer" value="2" optional="true" label="Specify minimum number of categories for FreeRate model"/>
386 <param argument="-cmax" type="integer" value="10" optional="true" label="Specify maximum number of categories for FreeRate model"/> 384 <param argument="-cmax" type="integer" value="10" optional="true" label="Specify maximum number of categories for FreeRate model"/>
387 <param argument="-merit" type="select" label="Specify either AIC, AICc or BIC for the optimality criterion to apply for new procedure" help=""> 385 <param argument="-merit" type="select" label="Specify either AIC, AICc or BIC for the optimality criterion to apply for new procedure" help="">
388 <option value="AIC">AIC</option> 386 <option value="AIC">AIC</option>
389 <option value="AICc">AICc</option> 387 <option value="AICc">AICc</option>
390 <option value="BIC">BIC</option> 388 <option value="BIC">BIC</option>
391 </param> 389 </param>
392 <param argument="-mtree" type="boolean" truevalue="-mtree" falsevalue="" checked="false" label="Turn on full tree search for each model considered, to obtain more accurate result"/> 390 <param argument="-mtree" type="boolean" truevalue="-mtree" falsevalue="" checked="false" label="Turn on full tree search for each model considered, to obtain more accurate result"/>
393 <param argument="-madd" type="text" optional="true" label="Specify a comma-separated list of mixture models to additionally consider for model selection" help="For example, -madd LG4M,LG4X to additionally include these two protein mixture models."> 391 <param argument="-madd" type="text" optional="true" label="Specify a comma-separated list of mixture models to additionally consider for model selection" help="For example, -madd LG4M,LG4X to additionally include these two protein mixture models.">
394 <sanitizer> 392 <expand macro="sanitize_query"
395 <valid initial="string.ascii_uppercase,string.digits,string.punctuation" /> 393 validinitial="string.ascii_uppercase,string.digits,string.punctuation" />
396 </sanitizer>
397 </param> 394 </param>
398 <param argument="-mdef" type="data" format="txt" optional="true" label="Specify a NEXUS model file to define new models."/> 395 <param argument="-mdef" type="data" format="txt" optional="true" label="Specify a NEXUS model file to define new models."/>
399 </section> 396 </section>
400 <section name="specifying_substitution" expanded="False" title="Specifying substitution models"> 397 <section name="specifying_substitution" expanded="False" title="Specifying substitution models">
401 <param argument="-mwopt" type="boolean" truevalue="-mwopt" falsevalue="" checked="false" label="Turn on optimizing weights of mixture models" help="Note that for models like LG+C20+F+G this mode is automatically turned on, but not for LG+C20+G."/> 398 <param argument="-mwopt" type="boolean" truevalue="-mwopt" falsevalue="" checked="false" label="Turn on optimizing weights of mixture models" help="Note that for models like LG+C20+F+G this mode is automatically turned on, but not for LG+C20+G."/>
402 </section> 399 </section>
403 <section name="rate_heterogeneity" expanded="False" title="Rate heterogeneity"> 400 <section name="rate_heterogeneity" expanded="False" title="Rate heterogeneity">
404 <param argument="-a" type="text" optional="true" label="Specify the Gamma shape parameter (default: estimate)"> 401 <param argument="-a" type="text" optional="true" label="Specify the Gamma shape parameter (default: estimate)">
405 <sanitizer> 402 <expand macro="sanitize_query" />
406 <valid initial="string.printable" />
407 </sanitizer>
408 </param> 403 </param>
409 <param argument="-gmedian" type="boolean" truevalue="-gmedian" falsevalue="" checked="false" label="Perform the median approximation for Gamma rate heterogeneity instead of the default mean approximation (Yang, 1994)"/> 404 <param argument="-gmedian" type="boolean" truevalue="-gmedian" falsevalue="" checked="false" label="Perform the median approximation for Gamma rate heterogeneity instead of the default mean approximation (Yang, 1994)"/>
410 <param argument="-i" type="text" optional="true" label="Specify the proportion of invariable sites (default: estimate)"> 405 <param argument="-i" type="text" optional="true" label="Specify the proportion of invariable sites (default: estimate)">
411 <sanitizer> 406 <expand macro="sanitize_query" />
412 <valid initial="string.printable" />
413 </sanitizer>
414 </param> 407 </param>
415 <param argument="--opt_gamma_inv" type="boolean" truevalue="--opt-gamma-inv" falsevalue="" checked="false" label="Perform more thorough estimation for +I+G model parameters"/> 408 <param argument="--opt_gamma_inv" type="boolean" truevalue="--opt-gamma-inv" falsevalue="" checked="false" label="Perform more thorough estimation for +I+G model parameters"/>
416 <param argument="-wsr" type="boolean" truevalue="-wsr" falsevalue="" checked="false" label="Write per-site rates to .rate file"/> 409 <param argument="-wsr" type="boolean" truevalue="-wsr" falsevalue="" checked="false" label="Write per-site rates to .rate file"/>
417 </section> 410 </section>
418 <section name="partition_model" expanded="False" title="Partition model options"> 411 <section name="partition_model" expanded="False" title="Partition model options">
498 <param argument="-bo" type="boolean" truevalue="-bo" falsevalue="" checked="false" label="Like -b but only perform bootstrap analysis (no analysis on original alignment and no consensus tree)."/> 491 <param argument="-bo" type="boolean" truevalue="-bo" falsevalue="" checked="false" label="Like -b but only perform bootstrap analysis (no analysis on original alignment and no consensus tree)."/>
499 </section> 492 </section>
500 </section> 493 </section>
501 <section name="miscellaneous_options" expanded="False" title="Miscellaneous options"> 494 <section name="miscellaneous_options" expanded="False" title="Miscellaneous options">
502 <param argument="-fconst" type="text" optional="true" label="Specify a list of comma-separated integer numbers" help="The number of entries should be equal to the number of states in the model (e.g. 4 for DNA and 20 for protein). IQ-TREE will then add a number of constant sites accordingly. For example, -fconst 10,20,15,40 will add 10 constant sites of all A, 20 constant sites of all C, 15 constant sites of all G and 40 constant sites of all T into the alignment."> 495 <param argument="-fconst" type="text" optional="true" label="Specify a list of comma-separated integer numbers" help="The number of entries should be equal to the number of states in the model (e.g. 4 for DNA and 20 for protein). IQ-TREE will then add a number of constant sites accordingly. For example, -fconst 10,20,15,40 will add 10 constant sites of all A, 20 constant sites of all C, 15 constant sites of all G and 40 constant sites of all T into the alignment.">
503 <sanitizer> 496 <expand macro="sanitize_query"
504 <valid initial="string.digits,string.punctuation" /> 497 validinitial="string.digits,string.punctuation" />
505 </sanitizer>
506 </param> 498 </param>
507 </section> 499 </section>
508 </inputs> 500 </inputs>
509 <outputs> 501 <outputs>
510 <data name='bionj' format='nhx' from_work_dir="*.bionj" label="${tool.name} on ${on_string}: BIONJ Tree" /> 502 <data name='bionj' format='nhx' from_work_dir="*.bionj" label="${tool.name} on ${on_string}: BIONJ Tree" />
639 <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" /> 631 <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
640 </assert_contents> 632 </assert_contents>
641 </output> 633 </output>
642 </test> 634 </test>
643 </tests> 635 </tests>
644 <help> 636 <help><![CDATA[
645 IQ-TREE 637 IQ-TREE
646 ======= 638 =======
647 639
648 The full documentation can be found here_. 640 The full documentation can be found here_.
649 641
920 +--| (93/98) 912 +--| (93/98)
921 +-----------Opossum 913 +-----------Opossum
922 914
923 915
924 From this figure, the branching patterns within reptiles are poorly supported (e.g. **Sphenodon** with SH-aLRT: 39%, UFBoot: 51% and **Turtle** with SH-aLRT: 85%, UFBoot: 72%) as well as the phylogenetic position of **Seal** within mammals (SH-aLRT: 68.3%, UFBoot: 75%). Other branches appear to be well supported. 916 From this figure, the branching patterns within reptiles are poorly supported (e.g. **Sphenodon** with SH-aLRT: 39%, UFBoot: 51% and **Turtle** with SH-aLRT: 85%, UFBoot: 72%) as well as the phylogenetic position of **Seal** within mammals (SH-aLRT: 68.3%, UFBoot: 75%). Other branches appear to be well supported.
925 </help> 917 ]]></help>
926 <citations> 918 <citations>
927 <citation type="doi">10.1093/molbev/msu300</citation> 919 <citation type="doi">10.1093/molbev/msu300</citation>
928 <citation type="doi">10.1093/molbev/mst024</citation> 920 <citation type="doi">10.1093/molbev/mst024</citation>
929 </citations> 921 </citations>
930 </tool> 922 </tool>