Mercurial > repos > azuzolo > qiime1_3_0
comparison qiime/make_phylogeny.xml @ 0:003162f90751 draft
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| author | azuzolo |
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| date | Wed, 06 Jun 2012 16:40:30 -0400 |
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| -1:000000000000 | 0:003162f90751 |
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| 1 <tool id="make_phylogeny" name="make_phylogeny" version="2.0.0"> | |
| 2 <description>Make Phylogeny</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">make_phylogeny.py</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 qiime_wrapper.py | |
| 8 --galaxy_inputdir='$__new_file_path__' | |
| 9 --galaxy_ext_change='$input_fp' | |
| 10 --galaxy_new_ext='fasta' | |
| 11 make_phylogeny.py | |
| 12 --input_fp='$__new_file_path__'/temporary.fasta | |
| 13 --tree_method=$tree_method | |
| 14 --result_fp=$result_fp | |
| 15 --log_fp=$log_fp | |
| 16 --root_method=$root_method</command> | |
| 17 <inputs> | |
| 18 <param name="input_fp" type="data" format="align" label="input_fp" | |
| 19 help="Path to read input alignment (output from filter_alignment) [REQUIRED]"/> | |
| 20 <param name="tree_method" type="select" label="tree_method" | |
| 21 help="Method for tree building. [default: fasttree]"> | |
| 22 <option value="clearcut">clearcut</option> | |
| 23 <option value="clustalw">clustalw</option> | |
| 24 <option value="raxml">raxml</option> | |
| 25 <option value="fasttree_v1">fasttree_v1</option> | |
| 26 <option value="fasttree" selected="true">fasttree</option> | |
| 27 <option value="muscle">muscle</option> | |
| 28 </param> | |
| 29 <param name="root_method" type="select" label="root_method" | |
| 30 help="method for choosing root of phylo tree [default: tree_method_default]"> | |
| 31 <option value="tree_method_default" selected="true">tree_method_default</option> | |
| 32 <option value="midpoint">midpoint</option> | |
| 33 </param> | |
| 34 </inputs> | |
| 35 <outputs> | |
| 36 <data format="tre" name="result_fp" label="${tool.name} on ${on_string}: tree" /> | |
| 37 <data format="txt" name="log_fp" label="${tool.name} on ${on_string}: log" /> | |
| 38 </outputs> | |
| 39 <tests> | |
| 40 </tests> | |
| 41 <help>For more information, see make_phylogeny_ in the Qiime documentation. | |
| 42 | |
| 43 Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA | |
| 44 | |
| 45 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN | |
| 46 | |
| 47 .. _make_phylogeny: http://qiime.org/scripts/make_phylogeny.html</help> | |
| 48 </tool> | |
| 49 |