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comparison iqtree.xml @ 4:f97743d52b87 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
author iuc
date Fri, 03 Apr 2020 09:04:30 -0400
parents 973a28be3b7f
children fc06db7794f1
comparison
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3:973a28be3b7f 4:f97743d52b87
2 <description>Phylogenomic / evolutionary tree construction from multiple sequences</description> 2 <description>Phylogenomic / evolutionary tree construction from multiple sequences</description>
3 <macros> 3 <macros>
4 <import>iqtree_macros.xml</import> 4 <import>iqtree_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors='exit_code' ><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 iqtree 8 iqtree
9 -pre PREF 9 -pre PREF
10 -nt \${GALAXY_SLOTS:-10} 10 #if $general_options.short_alignments:
11 -nt 1
12 #else:
13 -nt \${GALAXY_SLOTS:-10}
14 #end if
11 -redo 15 -redo
12 16
13 ## file 17 ## file
14 #if $general_options.s 18 #if $general_options.s
15 -s '$general_options.s' 19 -s '$general_options.s'
266 $bootstrap_parameters.nonparametric_bootstrap.bo 270 $bootstrap_parameters.nonparametric_bootstrap.bo
267 271
268 #if str($miscellaneous_options.fconst) != '' 272 #if str($miscellaneous_options.fconst) != ''
269 -fconst '$miscellaneous_options.fconst' 273 -fconst '$miscellaneous_options.fconst'
270 #end if 274 #end if
271
272 ]]> 275 ]]>
273 </command> 276 </command>
274 <inputs> 277 <inputs>
275 <section name="general_options" expanded="True" title="General options"> 278 <section name="general_options" expanded="true" title="General options">
276 <param argument="-s" type="data" format="txt" optional="true" label="Specify input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format."/> 279 <param argument="-s" type="data" format="txt" optional="true" label="Specify input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format."/>
280 <param type="boolean" name="short_alignments" truevalue="true" falsevalue="false" label="Short alignments" help="IQ-TREE will fail if given too many threads on input data that consists of short alignments, this option will force the use of a single thread." />
277 <param argument="-st" type="select" label="Specify sequence type as either of DNA, AA, BIN, MORPH, CODON or NT2AA for DNA, amino-acid, binary, morphological, codon or DNA-to-AA-translated sequences"> 281 <param argument="-st" type="select" label="Specify sequence type as either of DNA, AA, BIN, MORPH, CODON or NT2AA for DNA, amino-acid, binary, morphological, codon or DNA-to-AA-translated sequences">
278 <help><![CDATA[ 282 <help><![CDATA[
279 Note that -st CODON is always necessary when using codon models and you also need to specify a genetic code like this if differed from the standard genetic code. 283 Note that -st CODON is always necessary when using codon models and you also need to specify a genetic code like this if differed from the standard genetic code.
280 <br/><i>-st</i> NT2AA tells IQ-TREE to translate protein-coding DNA into AA sequences and then subsequent analysis will work on the AA sequences. You can also use a genetic code like -st NT2AA5 for the Invertebrate Mitochondrial Code (see genetic code table).]]> 284 <br/><i>-st</i> NT2AA tells IQ-TREE to translate protein-coding DNA into AA sequences and then subsequent analysis will work on the AA sequences. You can also use a genetic code like -st NT2AA5 for the Invertebrate Mitochondrial Code (see genetic code table).]]>
281 </help> 285 </help>
496 validinitial="string.digits,string.punctuation" /> 500 validinitial="string.digits,string.punctuation" />
497 </param> 501 </param>
498 </section> 502 </section>
499 </inputs> 503 </inputs>
500 <outputs> 504 <outputs>
501 <data name='bionj' format='nhx' from_work_dir="*.bionj" label="${tool.name} on ${on_string}: BIONJ Tree" /> 505 <data name="bionj" format="nhx" from_work_dir="*.bionj" label="${tool.name} on ${on_string}: BIONJ Tree" />
502 <data name='treefile' format='nhx' from_work_dir="*.treefile" label="${tool.name} on ${on_string}: MaxLikelihood Tree" /> 506 <data name="treefile" format="nhx" from_work_dir="*.treefile" label="${tool.name} on ${on_string}: MaxLikelihood Tree" />
503 <data name='contree' format='nhx' from_work_dir="*.contree" label="${tool.name} on ${on_string}: Consensus Tree" /> 507 <data name="contree" format="nhx" from_work_dir="*.contree" label="${tool.name} on ${on_string}: Consensus Tree" />
504 <data name='mldist' format='mldist' from_work_dir="*.mldist" label="${tool.name} on ${on_string}: MaxLikelihood Distance Matrix"/> 508 <data name="mldist" format="mldist" from_work_dir="*.mldist" label="${tool.name} on ${on_string}: MaxLikelihood Distance Matrix"/>
505 <data name='splits.nex' format='nex' from_work_dir="*.splits.nex" label="${tool.name} on ${on_string}: Occurence Frequencies in Bootstrap Trees" /> 509 <data name="splits.nex" format="nex" from_work_dir="*.splits.nex" label="${tool.name} on ${on_string}: Occurence Frequencies in Bootstrap Trees" />
506 <data name='iqtree' format='iqtree' from_work_dir="*.iqtree" label="${tool.name} on ${on_string}: Report and Final Tree" /> 510 <data name="iqtree" format="iqtree" from_work_dir="*.iqtree" label="${tool.name} on ${on_string}: Report and Final Tree" />
507 </outputs> 511 </outputs>
508 <tests> 512 <tests>
509 <test> 513 <test>
510 <param name="seed" value="1257" /> 514 <param name="seed" value="1257" />
511 <param name="st" value="AA" /> 515 <param name="st" value="AA" />
513 <param name="m" value="TESTNEW" /> 517 <param name="m" value="TESTNEW" />
514 <param name="msub" value="nuclear" /> 518 <param name="msub" value="nuclear" />
515 <param name="madd" value="LG4M,LG4X" /> 519 <param name="madd" value="LG4M,LG4X" />
516 <param name="merit" value="AICc" /> 520 <param name="merit" value="AICc" />
517 <param name="bb" value="1000" /> 521 <param name="bb" value="1000" />
518 <output name='bionj'> 522 <output name="bionj">
519 <assert_contents> 523 <assert_contents>
520 <has_text_matching expression=".*Human.*Whale.*" /> 524 <has_text_matching expression=".*Human.*Whale.*" />
521 </assert_contents> 525 </assert_contents>
522 </output> 526 </output>
523 <output name='iqtree'> 527 <output name="iqtree">
524 <assert_contents> 528 <assert_contents>
525 <has_text_matching expression="VT\+F\+R3(\s+((-|\d|\.)+))+" /> 529 <has_text_matching expression="VT\+F\+R3(\s+((-|\d|\.)+))+" />
526 </assert_contents> 530 </assert_contents>
527 </output> 531 </output>
528 <output name='mldist'> 532 <output name="mldist">
529 <assert_contents> 533 <assert_contents>
530 <has_line_matching expression="^Frog(\s+((\d|\.)+))+\s+$" /> 534 <has_line_matching expression="^Frog(\s+((\d|\.)+))+\s+$" />
531 <has_line_matching expression="^Whale(\s+((\d|\.)+))+\s+$" /> 535 <has_line_matching expression="^Whale(\s+((\d|\.)+))+\s+$" />
532 <has_line_matching expression="^Cow(\s+((\d|\.)+))+\s+$" /> 536 <has_line_matching expression="^Cow(\s+((\d|\.)+))+\s+$" />
533 </assert_contents> 537 </assert_contents>
534 </output> 538 </output>
535 <output name='treefile'> 539 <output name="treefile">
536 <assert_contents> 540 <assert_contents>
537 <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" /> 541 <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
538 </assert_contents> 542 </assert_contents>
539 </output> 543 </output>
540 <output name='contree' > 544 <output name="contree">
541 <assert_contents> 545 <assert_contents>
542 <has_line_matching 546 <has_line_matching
543 expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*\)\d+:(\d|\.)+,.*" /> 547 expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*\)\d+:(\d|\.)+,.*" />
544 </assert_contents> 548 </assert_contents>
545 </output> 549 </output>
546 <output name='splits.nex'> 550 <output name="splits.nex">
547 <assert_contents> 551 <assert_contents>
548 <has_line line="BEGIN Splits;" /> 552 <has_line line="BEGIN Splits;" />
549 <has_line line="END; [Splits]" /> 553 <has_line line="END; [Splits]" />
550 </assert_contents> 554 </assert_contents>
551 </output> 555 </output>
571 <param name="nm" value="1000" /> 575 <param name="nm" value="1000" />
572 <param name="bcor" value="0.99" /> 576 <param name="bcor" value="0.99" />
573 <param name="nstep" value="100" /> 577 <param name="nstep" value="100" />
574 <param name="beps" value="0.5" /> 578 <param name="beps" value="0.5" />
575 <param name="b" value="2" /> 579 <param name="b" value="2" />
576 <output name='iqtree'> 580 <output name="iqtree">
577 <assert_contents> 581 <assert_contents>
578 <has_text_matching expression="VT\+F\+I(\s+((-|\d|\.)+))+" /> 582 <has_text_matching expression="VT\+F\+I(\s+((-|\d|\.)+))+" />
579 </assert_contents> 583 </assert_contents>
580 </output> 584 </output>
581 <output name='treefile'> 585 <output name="treefile">
582 <assert_contents> 586 <assert_contents>
583 <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" /> 587 <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
584 </assert_contents> 588 </assert_contents>
585 </output> 589 </output>
586 </test> 590 </test>
605 <param name="nm" value="1000" /> 609 <param name="nm" value="1000" />
606 <param name="bcor" value="0.99" /> 610 <param name="bcor" value="0.99" />
607 <param name="nstep" value="100" /> 611 <param name="nstep" value="100" />
608 <param name="beps" value="0.5" /> 612 <param name="beps" value="0.5" />
609 <!-- <param name="b" value="100" /> --> 613 <!-- <param name="b" value="100" /> -->
610 <output name='iqtree'> 614 <output name="iqtree">
611 <assert_contents> 615 <assert_contents>
612 <has_text_matching expression="VT\+F\+I(\s+((-|\d|\.)+))+" /> 616 <has_text_matching expression="VT\+F\+I(\s+((-|\d|\.)+))+" />
613 </assert_contents> 617 </assert_contents>
614 </output> 618 </output>
615 <output name='treefile'> 619 <output name="treefile">
616 <assert_contents> 620 <assert_contents>
617 <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" /> 621 <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
618 </assert_contents> 622 </assert_contents>
619 </output> 623 </output>
620 </test> 624 </test>
621 <test> 625 <test>
622 <param name='s' value='example.phy' /> 626 <param name="s" value="example.phy" />
623 <output name='iqtree'> 627 <output name="iqtree">
624 <assert_contents> 628 <assert_contents>
625 <has_text_matching expression=".*Human.*Whale.*" /> 629 <has_text_matching expression=".*Human.*Whale.*" />
626 </assert_contents> 630 </assert_contents>
627 </output> 631 </output>
628 <output name='treefile'> 632 <output name="treefile">
629 <assert_contents> 633 <assert_contents>
630 <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" /> 634 <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
631 </assert_contents> 635 </assert_contents>
632 </output> 636 </output>
633 </test> 637 </test>
634 <test> 638 <test>
635 <param name='s' value='example.phy' /> 639 <param name="s" value="example.phy" />
636 <param name='opt_custommodel' value='true' /> 640 <param name="opt_custommodel" value="true" />
637 <param name='m' value='GTR+G{0.9}' /> 641 <param name="m" value="GTR+G{0.9}" />
638 <output name='iqtree'> 642 <output name="iqtree">
639 <assert_contents> 643 <assert_contents>
640 <has_text_matching expression=".*Human.*Whale.*" /> 644 <has_text_matching expression=".*Human.*Whale.*" />
641 </assert_contents> 645 </assert_contents>
642 </output> 646 </output>
643 <output name='treefile'> 647 <output name="treefile">
644 <assert_contents> 648 <assert_contents>
645 <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" /> 649 <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
646 </assert_contents> 650 </assert_contents>
647 </output> 651 </output>
652 </test>
653 <test>
654 <param name="s" value="short.fasta" />
655 <param name="short_alignments" value="true" />
648 </test> 656 </test>
649 </tests> 657 </tests>
650 <help><![CDATA[ 658 <help><![CDATA[
651 IQ-TREE 659 IQ-TREE
652 ======= 660 =======