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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="pick_rep_set" name="pick_rep_set" version="1.2.1">
2 <description>Pick representative set of sequences</description>
3 <requirements>
4 <requirement type="binary">pick_rep_set.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 pick_rep_set.py
9 --input_file=$input_file
10 --fasta_file=$fasta_file
11 --rep_set_picking_method=$rep_set_picking_method
12 --sort_by=$sort_by
13 --reference_seqs_fp=$reference_seqs_fp
14 --log_fp=$log_fp
15 --result_fp=$result_fp
16 </command>
17 <inputs>
18 <param name="input_file" type="data" format="qiimeotu" label="input_file"
19 help="Path to input otu mapping file [REQUIRED]"/>
20 <param name="reference_seqs_fp" type="data" format="fasta" optional="true" label="reference_seqs_fp"
21 help="collection of preferred representative sequences [default: ('NO', 'DEFAULT')]"/>
22 <param name="fasta_file" type="data" format="fasta" optional="true" label="fasta_file"
23 help="Path to input fasta file [REQUIRED if not picking against a reference set; default: None]"/>
24 <param name="rep_set_picking_method" type="select" label="rep_set_picking_method"
25 help="Method for picking representative sets. Valid choices are random, longest, most_abundant, first[default: first]">
26 <option value="random">random</option>
27 <option value="longest">longest</option>
28 <option value="most_abundant">most_abundant</option>
29 <option value="first" selected="true">first</option>
30 </param>
31 <param name="sort_by" type="select" value="otu" label="sort_by" >
32 <option value="otu" selected="true">otu</option>
33 <option value="seq_id">seq_id</option>
34 </param>
35
36 </inputs>
37 <outputs>
38 <data format="txt" name="log_fp" label="${tool.name} on ${on_string}: log" />
39 <data format="fasta" name="result_fp" label="${tool.name} on ${on_string}: rep_set.fasta" />
40 </outputs>
41 <tests>
42 </tests>
43 <help>
44
45 </help>
46 </tool>
47