Mercurial > repos > jjohnson > qiime
comparison alpha_diversity.xml @ 0:e5c3175506b7 default tip
Initial tool configs for qiime, most need work.
| author | Jim Johnson <jj@umn.edu> |
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| date | Sun, 17 Jul 2011 10:30:11 -0500 |
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| -1:000000000000 | 0:e5c3175506b7 |
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| 1 <tool id="alpha_diversity" name="alpha_diversity" version="1.2.0"> | |
| 2 <description>Calculate alpha diversity on each sample in an otu table, using a variety of alpha diversity metrics</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">alpha_diversity.py</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 qiime_wrapper.py | |
| 8 alpha_diversity.py | |
| 9 --input_path=$input_path | |
| 10 --output_path=$output_path | |
| 11 --metrics=$metrics | |
| 12 #if $tree_path.__str__ != "None" and len($tree_path.__str__) > 0: | |
| 13 --tree_path=$tree_path | |
| 14 #end if | |
| 15 | |
| 16 </command> | |
| 17 <inputs> | |
| 18 <param name="input_path" type="data" format="tabular" label="OTU table" | |
| 19 help="input path. directory for batch processing, filename for single file operation"/> | |
| 20 <param name="metrics" type="select" multiple="true" label="metrics" | |
| 21 help="metrics to use"> | |
| 22 <option value="ACE">ACE</option> | |
| 23 <option value="berger_parker_d">berger_parker_d</option> | |
| 24 <option value="brillouin_d">brillouin_d</option> | |
| 25 <option value="chao1">chao1</option> | |
| 26 <option value="chao1_confidence">chao1_confidence</option> | |
| 27 <option value="dominance">dominance</option> | |
| 28 <option value="doubles">doubles</option> | |
| 29 <option value="equitability">equitability</option> | |
| 30 <option value="fisher_alpha">fisher_alpha</option> | |
| 31 <option value="heip_e">heip_e</option> | |
| 32 <option value="kempton_taylor_q">kempton_taylor_q</option> | |
| 33 <option value="margalef">margalef</option> | |
| 34 <option value="mcintosh_d">mcintosh_d</option> | |
| 35 <option value="mcintosh_e">mcintosh_e</option> | |
| 36 <option value="menhinick">menhinick</option> | |
| 37 <option value="michaelis_menten_fit">michaelis_menten_fit</option> | |
| 38 <option value="observed_species">observed_species</option> | |
| 39 <option value="osd">osd</option> | |
| 40 <option value="reciprocal_simpson">reciprocal_simpson</option> | |
| 41 <option value="robbins">robbins</option> | |
| 42 <option value="shannon">shannon</option> | |
| 43 <option value="simpson">simpson</option> | |
| 44 <option value="simpson_e">simpson_e</option> | |
| 45 <option value="singles">singles</option> | |
| 46 <option value="strong">strong</option> | |
| 47 <option value="PD_whole_tree">PD_whole_tree</option> | |
| 48 </param> | |
| 49 <param name="tree_path" type="data" format="tre" label="tree_path" optional="true" | |
| 50 help="path to newick tree file, required for phylogenetic metrics: PD_whole_tree"/> | |
| 51 </inputs> | |
| 52 <outputs> | |
| 53 <data format="tabular" name="output_path" label="${tool.name} on ${on_string}: alpha_diversity"/> | |
| 54 </outputs> | |
| 55 <tests> | |
| 56 </tests> | |
| 57 <help> | |
| 58 | |
| 59 </help> | |
| 60 </tool> | |
| 61 |