Mercurial > repos > iuc > raxml
comparison raxml.xml @ 2:a4b71be30c3c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit 9f9e37b75ae2e5735289eeec1c74ff49e6e388e0"
author | iuc |
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date | Mon, 02 Dec 2019 07:52:10 -0500 |
parents | ba29b5e2a4be |
children | 14eb2acf30e3 |
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1:ba29b5e2a4be | 2:a4b71be30c3c |
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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> |