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comparison iqtree.xml @ 6:224c75ad0518 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
author iuc
date Thu, 12 Aug 2021 07:52:10 +0000
parents fc06db7794f1
children 524d31add34a
comparison
equal deleted inserted replaced
5:fc06db7794f1 6:224c75ad0518
292 292
293 #if str($tree_parameters.generating_random.r) != '' 293 #if str($tree_parameters.generating_random.r) != ''
294 -r '$tree_parameters.generating_random.r' 294 -r '$tree_parameters.generating_random.r'
295 #end if 295 #end if
296 296
297 $tree_parameters.generating_random.r 297 #if $tree_parameters.generating_random.rand
298 $tree_parameters.generating_random.rand 298 $tree_parameters.generating_random.rand
299 299 #end if
300 300
301 #if str($tree_parameters.generating_random.branch_min) != '' and str($tree_parameters.generating_random.branch_mean) != '' and str($tree_parameters.generating_random.branch_max) != '' 301 #if str($tree_parameters.generating_random.branch_min) != '' and str($tree_parameters.generating_random.branch_mean) != '' and str($tree_parameters.generating_random.branch_max) != ''
302 --rlen $tree_parameters.generating_random.branch_min $tree_parameters.generating_random.branch_mean $tree_parameters.generating_random.branch_max 302 --rlen $tree_parameters.generating_random.branch_min $tree_parameters.generating_random.branch_mean $tree_parameters.generating_random.branch_max
303 #end if 303 #end if
304 304
424 validinitial="string.ascii_uppercase,string.digits,string.punctuation" /> 424 validinitial="string.ascii_uppercase,string.digits,string.punctuation" />
425 </param> 425 </param>
426 </when> 426 </when>
427 <when value="false"> 427 <when value="false">
428 <param argument="-m" type="select" label="Perform standard model selection like jModelTest (for DNA) and ProtTest (for protein)" > 428 <param argument="-m" type="select" label="Perform standard model selection like jModelTest (for DNA) and ProtTest (for protein)" >
429 <help><![CDATA[
430 <b>Note:</b> Only <code>TEST</code> and custom models that do not rely on <code>MF</code> can be used in conjunction with bootstrap parameters (-b)<br/><br/>
431 IQ-TREE also works for codon, binary and morphogical data.
432 <table>
433 <tr>
434 <td><i>TESTONLY</i></td>
435 <td>Perform standard model selection like jModelTest (for DNA) and ProtTest (for protein). Moreover, IQ-TREE also works for codon, binary and morphogical data.</td>
436 </tr>
437 <tr>
438 <td><i>TEST</i></td>
439 <td>Like -m TESTONLY but immediately followed by tree reconstruction using the best-fit model found. So this performs both model selection and tree inference within a single run.</td>
440 </tr>
441 <tr>
442 <td><i>MF</i></td>
443 <td>Best-fit model selection without tree reconstruction.</td>
444 </tr>
445 <tr>
446 <td><i>MFP</i></td>
447 <td>Extended model selection with FreeRate heterogeneity immediately followed by tree inference.</td>
448 </tr>
449 </table>
450 ]]>
451 </help>
429 <option value="" selected="true">(None)</option> 452 <option value="" selected="true">(None)</option>
430 <option value="TESTONLY">Standard model selection</option> 453 <option value="TESTONLY">Standard model selection</option>
431 <option value="TEST">Standard model selection followed by tree inference</option> 454 <option value="TEST">Standard model selection followed by tree inference</option>
432 <option value="MF">Extended model selection with FreeRate heterogeneity</option> 455 <option value="MF">Extended model selection with FreeRate heterogeneity</option>
433 <option value="MFP">Extended model selection followed by tree inference</option> 456 <option value="MFP">Extended model selection followed by tree inference</option>
584 <param argument="--tree-dist2" type="data" format="nhx" optional="true" label="Like -rf but trees can have unequal taxon sets" /> 607 <param argument="--tree-dist2" type="data" format="nhx" optional="true" label="Like -rf but trees can have unequal taxon sets" />
585 608
586 </section> 609 </section>
587 <section name="generating_random" expanded="False" title="Generating random trees"> 610 <section name="generating_random" expanded="False" title="Generating random trees">
588 <param argument="-r" type="integer" optional="true" label="Specify number of taxa" help="IQ-TREE will create a random tree under Yule-Harding model with specified number of taxa"/> 611 <param argument="-r" type="integer" optional="true" label="Specify number of taxa" help="IQ-TREE will create a random tree under Yule-Harding model with specified number of taxa"/>
589 <param argument="--rand" type="boolean" truevalue="--rand UNI" falsevalue="" checked="false" label="Like -r, but a random tree is created under uniform model."/> 612 <param argument="--rand" type="select" optional="true" label="Random tree creation">
590 <param argument="--rand" type="boolean" truevalue="--rand CAT" falsevalue="" checked="false" label="Like -r, but a random caterpillar tree is created."/> 613 <option value="--rand UNI">Uniform model</option>
591 <param argument="--rand" type="boolean" truevalue="--rand BAL" falsevalue="" checked="false" label="Like -r, but a random balanced tree is created."/> 614 <option value="--rand CAT">Random caterpillar tree</option>
615 <option value="--rand BAL">Random balanced tree</option>
616 </param>
592 <param name="branch_min" type="integer" optional="true" label="Minimum branch lengths of the random tree" /> 617 <param name="branch_min" type="integer" optional="true" label="Minimum branch lengths of the random tree" />
593 <param name="branch_mean" type="integer" optional="true" label="Median branch lengths of the random tree" /> 618 <param name="branch_mean" type="integer" optional="true" label="Median branch lengths of the random tree" />
594 <param name="branch_max" type="integer" optional="true" label="Maximum branch lengths of the random tree" /> 619 <param name="branch_max" type="integer" optional="true" label="Maximum branch lengths of the random tree" />
595 </section> 620 </section>
596 <section name="ancestral_state" title="Ancestral State Reconstruction"> 621 <section name="ancestral_state" title="Ancestral State Reconstruction">
660 <data name="mlrate" format="data" from_work_dir="*.mlrate" label=""> 685 <data name="mlrate" format="data" from_work_dir="*.mlrate" label="">
661 <filter>modelling_parameters['rate_heterogeneity']['mlrate']</filter> 686 <filter>modelling_parameters['rate_heterogeneity']['mlrate']</filter>
662 </data> 687 </data>
663 </outputs> 688 </outputs>
664 <tests> 689 <tests>
665 <test> 690 <test expect_num_outputs="6">
666 <param name="seed" value="1257" /> 691 <param name="seed" value="1257" />
667 <param name="seqtype" value="AA" /> 692 <param name="seqtype" value="AA" />
668 <param name="s" value="example.phy" /> 693 <param name="s" value="example.phy" />
669 <param name="m" value="TEST" /> 694 <param name="m" value="TEST" />
670 <param name="msub" value="nuclear" /> 695 <param name="msub" value="nuclear" />
705 <has_line line="BEGIN Splits;" /> 730 <has_line line="BEGIN Splits;" />
706 <has_line line="END; [Splits]" /> 731 <has_line line="END; [Splits]" />
707 </assert_contents> 732 </assert_contents>
708 </output> 733 </output>
709 </test> 734 </test>
710 <test> 735 <test expect_num_outputs="6">
711 <!-- bootstrap sans model --> 736 <!-- bootstrap sans model -->
712 <param name="seed" value="1257" /> 737 <param name="seed" value="1257" />
713 <param name="seqtype" value="AA" /> 738 <param name="seqtype" value="AA" />
714 <param name="s" value="example.phy" /> 739 <param name="s" value="example.phy" />
715 <!-- <param name="m" value="TESTONLY" /> --> 740 <!-- <param name="m" value="TESTONLY" /> -->
739 <assert_contents> 764 <assert_contents>
740 <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" /> 765 <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
741 </assert_contents> 766 </assert_contents>
742 </output> 767 </output>
743 </test> 768 </test>
744 <test> 769 <test expect_num_outputs="6">
745 <!-- model sans bootstrap --> 770 <!-- model sans bootstrap -->
746 <param name="seed" value="1257" /> 771 <param name="seed" value="1257" />
747 <param name="seqtype" value="AA" /> 772 <param name="seqtype" value="AA" />
748 <param name="s" value="example.phy" /> 773 <param name="s" value="example.phy" />
749 <param name="m" value="TESTONLY" /> 774 <param name="m" value="TESTONLY" />
773 <assert_contents> 798 <assert_contents>
774 <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" /> 799 <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
775 </assert_contents> 800 </assert_contents>
776 </output> 801 </output>
777 </test> 802 </test>
778 <test> 803 <test expect_num_outputs="6">
779 <param name="s" value="example.phy" /> 804 <param name="s" value="example.phy" />
780 <output name="iqtree"> 805 <output name="iqtree">
781 <assert_contents> 806 <assert_contents>
782 <has_text_matching expression=".*Human.*Whale.*" /> 807 <has_text_matching expression=".*Human.*Whale.*" />
783 </assert_contents> 808 </assert_contents>
786 <assert_contents> 811 <assert_contents>
787 <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" /> 812 <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
788 </assert_contents> 813 </assert_contents>
789 </output> 814 </output>
790 </test> 815 </test>
791 <test> 816 <test expect_num_outputs="6">
792 <param name="s" value="example.phy" /> 817 <param name="s" value="example.phy" />
793 <param name="opt_custommodel" value="true" /> 818 <param name="opt_custommodel" value="true" />
794 <param name="m" value="GTR+G{0.9}" /> 819 <param name="m" value="GTR+G{0.9}" />
795 <output name="iqtree"> 820 <output name="iqtree">
796 <assert_contents> 821 <assert_contents>
801 <assert_contents> 826 <assert_contents>
802 <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" /> 827 <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
803 </assert_contents> 828 </assert_contents>
804 </output> 829 </output>
805 </test> 830 </test>
806 <test> 831 <test expect_num_outputs="6">
807 <param name="s" value="short.fasta" /> 832 <param name="s" value="short.fasta" />
808 <param name="short_alignments" value="true" /> 833 <param name="short_alignments" value="true" />
809 <output name="treefile"> 834 <output name="treefile">
810 <assert_contents> 835 <assert_contents>
811 <has_line_matching expression="\(NC_045512.+\(MT019531.+MT019532.+" /> 836 <has_line_matching expression="\(NC_045512.+\(MT019531.+MT019532.+" />