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comparison iqtree.xml @ 7:cef78e63f746 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
author iuc
date Fri, 13 Aug 2021 21:35:22 +0000
parents 5cd49ec56116
children 2e0636f07c37
comparison
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6:5cd49ec56116 7:cef78e63f746
18 ## file 18 ## file
19 #if $general_options.s 19 #if $general_options.s
20 -s '$general_options.s' 20 -s '$general_options.s'
21 #end if 21 #end if
22 22
23 #if $general_options.o
24 -o '$general_options.o'
25 #end if
26
23 ## file 27 ## file
24 #if $general_options.t 28 #if $general_options.t
25 -t '$general_options.t' 29 -t '$general_options.t'
26 $tree_parameters.constructing_consensus.con_tree 30 $tree_parameters.constructing_consensus.con_tree
27 $tree_parameters.constructing_consensus.con_net 31 $tree_parameters.constructing_consensus.con_net
361 ]]> 365 ]]>
362 </command> 366 </command>
363 <inputs> 367 <inputs>
364 <section name="general_options" expanded="true" title="General options"> 368 <section name="general_options" expanded="true" title="General options">
365 <param argument="-s" type="data" format="txt" optional="true" label="Specify input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format."/> 369 <param argument="-s" type="data" format="txt" optional="true" label="Specify input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format."/>
366 <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." /> 370 <param argument="-o" type="text" optional="true" label="Comma-separated list of taxons to output">
371 <expand macro="sanitize_query" />
372 </param>
373
374 <param type="boolean" name="short_alignments" 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." />
367 <param argument="--seqtype" 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"> 375 <param argument="--seqtype" 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">
368 <help><![CDATA[ 376 <help><![CDATA[
369 Note that --seqtype 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. 377 Note that --seqtype 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.
370 <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 --seqtype NT2AA5 for the Invertebrate Mitochondrial Code (see genetic code table).]]> 378 <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 --seqtype NT2AA5 for the Invertebrate Mitochondrial Code (see genetic code table).]]>
371 </help> 379 </help>
680 <data name="treefile" format="nhx" from_work_dir="*.treefile" label="${tool.name} on ${on_string}: MaxLikelihood Tree" /> 688 <data name="treefile" format="nhx" from_work_dir="*.treefile" label="${tool.name} on ${on_string}: MaxLikelihood Tree" />
681 <data name="contree" format="nhx" from_work_dir="*.contree" label="${tool.name} on ${on_string}: Consensus Tree" /> 689 <data name="contree" format="nhx" from_work_dir="*.contree" label="${tool.name} on ${on_string}: Consensus Tree" />
682 <data name="mldist" format="mldist" from_work_dir="*.mldist" label="${tool.name} on ${on_string}: MaxLikelihood Distance Matrix"/> 690 <data name="mldist" format="mldist" from_work_dir="*.mldist" label="${tool.name} on ${on_string}: MaxLikelihood Distance Matrix"/>
683 <data name="splits" format="nex" from_work_dir="*.splits.nex" label="${tool.name} on ${on_string}: Occurence Frequencies in Bootstrap Trees" /> 691 <data name="splits" format="nex" from_work_dir="*.splits.nex" label="${tool.name} on ${on_string}: Occurence Frequencies in Bootstrap Trees" />
684 <data name="iqtree" format="iqtree" from_work_dir="*.iqtree" label="${tool.name} on ${on_string}: Report and Final Tree" /> 692 <data name="iqtree" format="iqtree" from_work_dir="*.iqtree" label="${tool.name} on ${on_string}: Report and Final Tree" />
685 <data name="mlrate" format="data" from_work_dir="*.mlrate" label=""> 693 <data name="mlrate" format="data" from_work_dir="*.mlrate" label="${tool.name} on ${on_string}: ML Rates">
686 <filter>modelling_parameters['rate_heterogeneity']['mlrate']</filter> 694 <filter>modelling_parameters['rate_heterogeneity']['mlrate']</filter>
695 </data>
696 <data name="timetree" format="nex" from_work_dir="PREF.timetree.nex" label="${tool.name} on ${on_string}: Tree labeled with dates">
697 <filter>time_tree['date_source']['select_source'] != 'none'</filter>
687 </data> 698 </data>
688 </outputs> 699 </outputs>
689 <tests> 700 <tests>
690 <test expect_num_outputs="6"> 701 <test expect_num_outputs="6">
691 <param name="seed" value="1257" /> 702 <param name="seed" value="1257" />
832 <param name="s" value="short.fasta" /> 843 <param name="s" value="short.fasta" />
833 <param name="short_alignments" value="true" /> 844 <param name="short_alignments" value="true" />
834 <output name="treefile"> 845 <output name="treefile">
835 <assert_contents> 846 <assert_contents>
836 <has_line_matching expression="\(NC_045512.+\(MT019531.+MT019532.+" /> 847 <has_line_matching expression="\(NC_045512.+\(MT019531.+MT019532.+" />
848 </assert_contents>
849 </output>
850 </test>
851 <test expect_num_outputs="7">
852 <param name="s" value="dates.fa" />
853 <param name="n" value="100" />
854 <param name="seed" value="122125" />
855 <param name="select_source" value="dataset" />
856 <param name="date" value="dates.tabular" />
857 <output name="timetree">
858 <assert_contents>
859 <has_line_matching expression=".+222-3pu_03-28-01_985737600.+" />
837 </assert_contents> 860 </assert_contents>
838 </output> 861 </output>
839 </test> 862 </test>
840 </tests> 863 </tests>
841 <help><![CDATA[ 864 <help><![CDATA[