Mercurial > repos > jjohnson > qiime
comparison trim_sff_primers.xml @ 0:e5c3175506b7 default tip
Initial tool configs for qiime, most need work.
author | Jim Johnson <jj@umn.edu> |
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date | Sun, 17 Jul 2011 10:30:11 -0500 |
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-1:000000000000 | 0:e5c3175506b7 |
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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 |