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Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
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1 <tool id="filter_otu_table" name="filter_otu_table" version="1.2.0">
2 <description>Filters OTU table by minimum OTU count and number of samples or by taxonomy</description>
3 <requirements>
4 <requirement type="binary">filter_otu_table.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 --galaxy_tmpdir='$__new_file_path__'
9 filter_otu_table.py
10 --otu_table_fp=$otu_table_fp
11 --min_count=$min_count
12 --min_samples=$min_samples
13 --include_taxonomy=$include_taxonomy
14 --exclude_taxonomy=$exclude_taxonomy
15 --dir_path=$dir_path
16 --seqs_per_sample=$seqs_per_sample
17 </command>
18 <inputs>
19 <param name="otu_table_fp" type="data" format="txt" label="otu_table_fp"
20 help="path to the input OTU table (i.e., the output from make_otu_table.py) [REQUIRED]"/>
21 <param name="min_count" type="integer" value="1" label="min_count"
22 help="retain OTUs with at least this many sequences [default=1]"/>
23 <param name="min_samples" type="integer" value="2" label="min_samples"
24 help="retain OTUs found in at least this many samples [default=2]"/>
25 <param name="include_taxonomy" type="text" value="" label="include_taxonomy"
26 help="list of taxonomy terms to include [default=]"/>
27 <param name="exclude_taxonomy" type="text" value="" label="exclude_taxonomy"
28 help="list of taxonomy terms to exclude [default=]"/>
29 <param name="dir_path" type="text" value="./" label="dir_path"
30 help="directory prefix for all analyses [default=./]"/>
31 <param name="seqs_per_sample" type="integer" value="-1" label="seqs_per_sample"
32 help="minimum sequences per sample to retain the sample. [default=('NO', 'DEFAULT')]"/>
33 </inputs>
34 <outputs>
35
36 </outputs>
37 <tests>
38 </tests>
39 <help>
40
41 </help>
42 </tool>
43