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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="process_sff" name="process_sff" version="1.2.0">
2 <description>Convert sff to FASTA and QUAL files</description>
3 <requirements>
4 <requirement type="binary">process_sff.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 --galaxy_tmpdir='$__new_file_path__'
9 process_sff.py
10 --input_dir=$input_dir
11 $make_flowgram
12 $convert_to_FLX
13 $use_sfftools
14 --output_dir=$__new_file_path__
15 </command>
16 <inputs>
17 <param name="input_dir" type="text" label="input_dir"
18 help="Input directory of sff files [REQUIRED]"/>
19 <param name="make_flowgram" type="boolean" truevalue="--make_flowgram" falsevalue="" checked="false" label="make_flowgram"
20 help="generate a flowgram file. [default: False]"/>
21 <param name="convert_to_FLX" type="boolean" truevalue="--convert_to_FLX" falsevalue="" checked="false" label="convert_to_FLX"
22 help="convert Titanium reads to FLX length. [default: False]"/>
23 <param name="use_sfftools" type="boolean" truevalue="--use_sfftools" falsevalue="" checked="false" label="use_sfftools"
24 help="use the external programs sfffile and sffinfo for processing, instead of the equivalent python implementation"/>
25 </inputs>
26 <outputs>
27
28 </outputs>
29 <tests>
30 </tests>
31 <help>
32
33 </help>
34 </tool>
35