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comparison iqtree.xml @ 8:2e0636f07c37 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit a58c8d3c985688e49908dfeceab5be4352d71563"
author iuc
date Wed, 18 Aug 2021 20:41:14 +0000
parents cef78e63f746
children 35129e963633
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7:cef78e63f746 8:2e0636f07c37
74 #end if 74 #end if
75 75
76 ## date options 76 ## date options
77 #if str($time_tree.date_source.select_source) == 'dataset': 77 #if str($time_tree.date_source.select_source) == 'dataset':
78 #if $time_tree.date_source.date: 78 #if $time_tree.date_source.date:
79 --date $time_tree.date_source.date 79 --date '$time_tree.date_source.date'
80 #end if 80 #end if
81 #elif str($time_tree.date_source.select_source) == 'input': 81 #elif str($time_tree.date_source.select_source) == 'input':
82 --date TAXNAME 82 --date TAXNAME
83 #if str($time_tree.date_source.date_tip) != '': 83 #if str($time_tree.date_source.date_tip) != '':
84 --date-tip '$time_tree.date_source.date_tip' 84 --date-tip '$time_tree.date_source.date_tip'
364 #end if 364 #end if
365 ]]> 365 ]]>
366 </command> 366 </command>
367 <inputs> 367 <inputs>
368 <section name="general_options" expanded="true" title="General options"> 368 <section name="general_options" expanded="true" title="General options">
369 <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,fasta,phylip,nex,clustal,msf" optional="true" label="Specify input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format."/>
370 <param argument="-o" type="text" optional="true" label="Comma-separated list of taxons to output"> 370 <param argument="-o" type="text" optional="true" label="Comma-separated list of taxons to output">
371 <expand macro="sanitize_query" /> 371 <expand macro="sanitize_query" />
372 </param> 372 </param>
373 373
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." /> 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." />
398 <option value="input">Derive from input</option> 398 <option value="input">Derive from input</option>
399 </param> 399 </param>
400 <when value="none" /> 400 <when value="none" />
401 <when value="input" /> 401 <when value="input" />
402 <when value="dataset"> 402 <when value="dataset">
403 <param argument="--date" type="data" format="text" optional="true" label="File containing dates of tips or ancestral nodes" /> 403 <param argument="--date" type="data" format="txt,tabular" optional="true" label="File containing dates of tips or ancestral nodes" />
404 </when> 404 </when>
405 </conditional> 405 </conditional>
406 <param argument="--date-tip" type="text" optional="true" label="Tip dates as a real number or YYYY-MM-DD"> 406 <param argument="--date-tip" type="text" optional="true" label="Tip dates as a real number or YYYY-MM-DD">
407 <expand macro="sanitize_query" /> 407 <expand macro="sanitize_query" />
408 </param> 408 </param>