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comparison raxml.xml @ 5:d38fcf1b83c5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit 9f9e37b75ae2e5735289eeec1c74ff49e6e388e0"
author iuc
date Mon, 02 Dec 2019 12:51:50 +0000
parents 58a0f16c950c
children 26875a61191d
comparison
equal deleted inserted replaced
4:58a0f16c950c 5:d38fcf1b83c5
1 <tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="8.2.4"> 1 <tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="8.2.4+galaxy1">
2 <description>- Maximum Likelihood based inference of large phylogenetic trees</description> 2 <description>- Maximum Likelihood based inference of large phylogenetic trees</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="8.2.4">raxml</requirement> 4 <requirement type="package" version="8.2.4">raxml</requirement>
5 <requirement type="package" version="3.6">python</requirement>
5 </requirements> 6 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
7 ## binary is hard-coded to the pthreads enabled raxml executable if threads > 1 8 ## binary is hard-coded to the pthreads enabled raxml executable if threads > 1
8 #set $slots = $getVar('GALAXY_SLOTS', 1) 9 #set $slots = $getVar('GALAXY_SLOTS', 1)
9 #if $slots == 1: 10 #if $slots == 1:
445 <test> 446 <test>
446 <param name="extraOptions" value="required"/> 447 <param name="extraOptions" value="required"/>
447 <param name="infile" value="dna.phy"/> 448 <param name="infile" value="dna.phy"/>
448 <param name="model_type" value="nucleotide"/> 449 <param name="model_type" value="nucleotide"/>
449 <param name="base_model" value="GTRCAT"/> 450 <param name="base_model" value="GTRCAT"/>
450 <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.basic" /> 451 <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.basic" ftype="nhx" />
451 <output name="bestTree"> 452 <output name="bestTree" ftype="nhx">
452 <assert_contents> 453 <assert_contents>
453 <has_text_matching expression="Frog" /> 454 <has_text_matching expression="Frog" />
454 </assert_contents> 455 </assert_contents>
455 </output> 456 </output>
456 </test> 457 </test>
458 <param name="extraOptions" value="full"/> 459 <param name="extraOptions" value="full"/>
459 <param name="infile" value="dna.fasta"/> 460 <param name="infile" value="dna.fasta"/>
460 <param name="model_type" value="nucleotide"/> 461 <param name="model_type" value="nucleotide"/>
461 <param name="base_model" value="GTRCAT"/> 462 <param name="base_model" value="GTRCAT"/>
462 <param name="number_of_runs" value="5"/> 463 <param name="number_of_runs" value="5"/>
463 <output name="parsimonyTree"> 464 <output name="parsimonyTree" ftype="nhx">
464 <assert_contents> 465 <assert_contents>
465 <has_text_matching expression="Chicken" /> 466 <has_text_matching expression="Chicken" />
466 <has_text_matching expression="RUN.4" />
467 </assert_contents> 467 </assert_contents>
468 </output> 468 </output>
469 <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.multi" lines_diff="30"/> 469 <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.multi" ftype="nhx"/>
470 <output name="bestTree"> 470 <output name="bestTree" ftype="nhx">
471 <assert_contents> 471 <assert_contents>
472 <has_text_matching expression="Whale" /> 472 <has_text_matching expression="Whale" />
473 </assert_contents> 473 </assert_contents>
474 </output> 474 </output>
475 </test> 475 </test>