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comparison iqtree.xml @ 3:973a28be3b7f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
author iuc
date Wed, 29 Jan 2020 16:34:20 -0500
parents d1c340a5664b
children f97743d52b87
comparison
equal deleted inserted replaced
2:d1c340a5664b 3:973a28be3b7f
1 <tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@.1" > 1 <tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@.3" >
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" />
301 <section name="automatic_model" expanded="False" title="Automatic model selection"> 301 <section name="automatic_model" expanded="False" title="Automatic model selection">
302 <conditional name="cond_model" > 302 <conditional name="cond_model" >
303 <param name="opt_custommodel" type="boolean" checked="false" label="Use Custom Model" help="See http://www.iqtree.org/doc/Substitution-Models"/> 303 <param name="opt_custommodel" type="boolean" checked="false" label="Use Custom Model" help="See http://www.iqtree.org/doc/Substitution-Models"/>
304 <when value="true"> 304 <when value="true">
305 <param argument="-m" type="text" label="Model"> 305 <param argument="-m" type="text" label="Model">
306 <sanitizer> 306 <expand macro="sanitize_query"
307 <valid initial="string.ascii_uppercase,+" /> 307 validinitial="string.ascii_uppercase,string.digits,string.punctuation" />
308 </sanitizer>
309 </param> 308 </param>
310 </when> 309 </when>
311 <when value="false"> 310 <when value="false">
312 <param argument="-m" type="select" label="Perform standard model selection like jModelTest (for DNA) and ProtTest (for protein)" > 311 <param argument="-m" type="select" label="Perform standard model selection like jModelTest (for DNA) and ProtTest (for protein)" >
313 <help><![CDATA[ 312 <help><![CDATA[
630 <assert_contents> 629 <assert_contents>
631 <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" /> 630 <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
632 </assert_contents> 631 </assert_contents>
633 </output> 632 </output>
634 </test> 633 </test>
634 <test>
635 <param name='s' value='example.phy' />
636 <param name='opt_custommodel' value='true' />
637 <param name='m' value='GTR+G{0.9}' />
638 <output name='iqtree'>
639 <assert_contents>
640 <has_text_matching expression=".*Human.*Whale.*" />
641 </assert_contents>
642 </output>
643 <output name='treefile'>
644 <assert_contents>
645 <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
646 </assert_contents>
647 </output>
648 </test>
635 </tests> 649 </tests>
636 <help><![CDATA[ 650 <help><![CDATA[
637 IQ-TREE 651 IQ-TREE
638 ======= 652 =======
639 653