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comparison iqtree.xml @ 12:df8bf04acdb1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3b1c44e42b042ccbbe2d9e01c77d18f109d4984f"
author iuc
date Sat, 27 Nov 2021 09:44:25 +0000
parents d460875c806a
children 9454e1c4f022
comparison
equal deleted inserted replaced
11:d460875c806a 12:df8bf04acdb1
1 <tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@+@VERSION_SUFFIX@" > 1 <tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
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 <token name="@VERSION_SUFFIX@">galaxy2</token>
5 <import>iqtree_macros.xml</import> 4 <import>iqtree_macros.xml</import>
6 </macros> 5 </macros>
7 <expand macro="requirements" /> 6 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
9 iqtree 8 iqtree
21 #end if 20 #end if
22 21
23 #if $general_options.o 22 #if $general_options.o
24 -o '$general_options.o' 23 -o '$general_options.o'
25 #end if 24 #end if
26 25 --seqtype $general_options.seqtype
27 ## file 26 ## file
28 #if $general_options.t 27 #if $general_options.t
29 -t '$general_options.t' 28 -t '$general_options.t'
30 $tree_parameters.constructing_consensus.contree 29 $tree_parameters.constructing_consensus.contree
31 $tree_parameters.constructing_consensus.connet 30 $tree_parameters.constructing_consensus.connet
543 <option value="Q">Edge-unlinked proportional partition model</option> 542 <option value="Q">Edge-unlinked proportional partition model</option>
544 <option value="S">Separate tree inference</option> 543 <option value="S">Separate tree inference</option>
545 </param> 544 </param>
546 <when value="none" /> 545 <when value="none" />
547 <when value="p"> 546 <when value="p">
548 <param argument="-p" type="data" format="nex" optional="true" label="Partition file" /> 547 <param argument="-p" name="model_file" type="data" format="nex" optional="true" label="Partition file" />
549 <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" /> 548 <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" />
550 <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" /> 549 <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" />
551 </when> 550 </when>
552 <when value="q"> 551 <when value="q">
553 <param argument="-q" type="data" format="nex" optional="true" label="Partition file" /> 552 <param argument="-q" name="model_file" type="data" format="nex" optional="true" label="Partition file" />
554 <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" /> 553 <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" />
555 <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" /> 554 <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" />
556 </when> 555 </when>
557 <when value="Q"> 556 <when value="Q">
558 <param argument="-Q" type="data" format="nex" optional="true" label="Partition file" /> 557 <param argument="-Q" name="model_file" type="data" format="nex" optional="true" label="Partition file" />
559 <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" /> 558 <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" />
560 <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" /> 559 <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" />
561 </when> 560 </when>
562 <when value="S"> 561 <when value="S">
563 <param argument="-S" type="data" format="nex" optional="true" label="Partition file" /> 562 <param argument="-S" name="model_file" type="data" format="nex" optional="true" label="Partition file" />
564 <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" /> 563 <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" />
565 <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" /> 564 <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" />
566 </when> 565 </when>
567 </conditional> 566 </conditional>
568 </section> 567 </section>
703 </data> 702 </data>
704 </outputs> 703 </outputs>
705 <tests> 704 <tests>
706 <test expect_num_outputs="5"> 705 <test expect_num_outputs="5">
707 <param name="seed" value="1257" /> 706 <param name="seed" value="1257" />
708 <param name="seqtype" value="AA" /> 707 <param name="seqtype" value="DNA" />
709 <param name="s" value="example.phy" /> 708 <param name="s" value="example.phy" />
710 <param name="m" value="TEST" /> 709 <param name="m" value="TEST" />
711 <param name="msub" value="nuclear" /> 710 <param name="msub" value="nuclear" />
712 <param name="madd" value="LG4M,LG4X" /> 711 <param name="madd" value="LG4M,LG4X" />
713 <param name="merit" value="AICc" /> 712 <param name="merit" value="AICc" />
749 </output> 748 </output>
750 </test> 749 </test>
751 <test expect_num_outputs="5"> 750 <test expect_num_outputs="5">
752 <!-- bootstrap sans model --> 751 <!-- bootstrap sans model -->
753 <param name="seed" value="1257" /> 752 <param name="seed" value="1257" />
754 <param name="seqtype" value="AA" /> 753 <param name="seqtype" value="DNA" />
755 <param name="s" value="example.phy" /> 754 <param name="s" value="example.phy" />
756 <!-- <param name="m" value="TESTONLY" /> --> 755 <!-- <param name="m" value="TESTONLY" /> -->
757 <param name="msub" value="nuclear" /> 756 <param name="msub" value="nuclear" />
758 <param name="cmin" value="2" /> 757 <param name="cmin" value="2" />
759 <param name="cmax" value="10" /> 758 <param name="cmax" value="10" />
783 </output> 782 </output>
784 </test> 783 </test>
785 <test expect_num_outputs="5"> 784 <test expect_num_outputs="5">
786 <!-- model sans bootstrap --> 785 <!-- model sans bootstrap -->
787 <param name="seed" value="1257" /> 786 <param name="seed" value="1257" />
788 <param name="seqtype" value="AA" /> 787 <param name="seqtype" value="DNA" />
789 <param name="s" value="example.phy" /> 788 <param name="s" value="example.phy" />
790 <param name="m" value="TESTONLY" /> 789 <param name="m" value="TESTONLY" />
791 <param name="msub" value="nuclear" /> 790 <param name="msub" value="nuclear" />
792 <param name="cmin" value="2" /> 791 <param name="cmin" value="2" />
793 <param name="cmax" value="10" /> 792 <param name="cmax" value="10" />