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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="trim_sff_primers" name="trim_sff_primers" version="1.2.0">
2 <description>Trim sff primers</description>
3 <requirements>
4 <requirement type="binary">trim_sff_primers.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 --galaxy_tmpdir='$__new_file_path__'
9 trim_sff_primers.py
10 --libdir=$libdir
11 --input_map=$input_map
12 --sfffile_path=$sfffile_path
13 --sffinfo_path=$sffinfo_path
14 $use_sfftools
15 $debug
16 </command>
17 <inputs>
18 <param name="libdir" type="text" label="libdir"
19 help="The directory containing per-library sff files [REQUIRED]"/>
20 <param name="input_map" type="data" format="tabular" label="input_map"
21 help="Path to the input mapping file describing the libraries [REQUIRED]"/>
22 <param name="sfffile_path" type="text" value="sfffile" label="sfffile_path"
23 help="Path to sfffile binary [default: sfffile]"/>
24 <param name="sffinfo_path" type="text" value="sffinfo" label="sffinfo_path"
25 help="Path to sffinfo binary [default: sffinfo]"/>
26 <param name="use_sfftools" type="boolean" truevalue="--use_sfftools" falsevalue="" checked="false" label="use_sfftools"
27 help="Use external sffinfo and sfffile programs instead of equivalent Python implementation."/>
28 <param name="debug" type="boolean" truevalue="--debug" falsevalue="" checked="false" label="debug"
29 help="Print command-line output for debugging [default: False]"/>
30 </inputs>
31 <outputs>
32
33 </outputs>
34 <tests>
35 </tests>
36 <help>
37
38 </help>
39 </tool>
40