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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_by_metadata" name="filter_by_metadata" version="1.2.0">
2 <description>Filter OTU table by removal of specified metadata</description>
3 <requirements>
4 <requirement type="binary">filter_by_metadata.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 --galaxy_tmpdir='$__new_file_path__'
9 filter_by_metadata.py
10 --otu_table_fp=$otu_table_fp
11 --map=$map
12 --states=$states
13 --otu_outfile=$otu_outfile
14 --map_outfile=$map_outfile
15 --num_seqs_per_otu=$num_seqs_per_otu
16 </command>
17 <inputs>
18 <param name="otu_table_fp" type="data" format="txt" label="otu_table_fp"
19 help="path to the input OTU table (i.e., the output from make_otu_table.py) [REQUIRED]"/>
20 <param name="map" type="data" format="tabular" label="map"
21 help="path to the map file [REQUIRED]"/>
22 <param name="states" type="text" label="states"
23 help="string containing valid states, e.g. 'STUDY_NAME:DOG' [REQUIRED]"/>
24 <param name="num_seqs_per_otu" type="integer" value="1" label="num_seqs_per_otu"
25 help="minimum counts across samples to keep OTU, default is only to keep OTUs that are present in the samples."/>
26 </inputs>
27 <outputs>
28 <data format="txt" name="otu_outfile"/>
29 <data format="txt" name="map_outfile"/>
30 </outputs>
31 <tests>
32 </tests>
33 <help>
34
35 </help>
36 </tool>
37