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comparison qiime/make_otu_table.xml @ 0:003162f90751 draft

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author azuzolo
date Wed, 06 Jun 2012 16:40:30 -0400
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1 <tool id="make_otu_table" name="make_otu_table" version="2.0.0">
2 <description>Make OTU table</description>
3 <requirements>
4 <requirement type="binary">make_otu_table.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 make_otu_table.py
9 --otu_map_fp=$otu_map_fp
10 --output_fp=$output_fp
11 #if $taxonomy.__str__ != 'None':
12 --taxonomy=$taxonomy
13 #end if
14 #if $exclude_otus_fp.__str__ != 'None':
15 --exclude_otus_fp=$exclude_otus_fp
16 #end if
17 </command>
18 <inputs>
19 <param name="otu_map_fp" type="data" format="qiimeotu" label="otu_map_fp"
20 help="path to the input OTU map (i.e., the output from pick_otus.py) [REQUIRED]"/>
21 <param name="taxonomy" type="data" format="seq.taxonomy" optional="true" label="taxonomy"
22 help="Path to taxonomy assignment, containing the assignments of taxons to sequences (i.e., resulting txt file from assign_taxonomy.py) [OPTIONAL]"/>
23 <param name="exclude_otus_fp" type="data" format="txt" optional="true" label="exclude_otus_fp"
24 help="a filepath listing OTU identifiers that should not be included in the OTU table (e.g., the output of identify_chimeric_seqs.py) or a fasta file where seq ids should be excluded (e.g., failures fasta file from align_seqs.py) [OPTIONAL]"/>
25 </inputs>
26 <outputs>
27 <data format="qiimeotutable" name="output_fp" label="${tool.name} on ${on_string}: otu_table"/>
28 </outputs>
29 <tests>
30 </tests>
31 <help>For more information, see make_otu_table_ in the Qiime documentation.
32
33 Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA
34
35 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
36
37 .. _make_otu_table: http://qiime.org/scripts/make_otu_table</help>
38 </tool>
39