comparison denoise.xml @ 0:e5c3175506b7 default tip

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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-1:000000000000 0:e5c3175506b7
1 <tool id="denoise" name="denoise" version="1.2.0">
2 <description>Denoise a flowgram file</description>
3 <requirements>
4 <requirement type="binary">denoise.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 --galaxy_tmpdir='$__new_file_path__'
9 denoise.py
10 --input_file=$input_file
11 --fasta_file=$fasta_file
12 --output_dir=$__new_file_path__
13 --method=$method
14 $keep_intermediates
15 --cut-off=$cut_off
16 --precision=$precision
17 --num_cpus=$num_cpus
18 $force_overwrite
19 --map_fname=$map_fname
20 --primer=$primer
21 </command>
22 <inputs>
23 <param name="input_file" type="data" format="txt" label="input_file"
24 help="path to flowgram files (.sff.txt), comma separated [REQUIRED]"/>
25 <param name="fasta_file" type="data" format="fasta" label="fasta_file"
26 help="path to fasta file from split_libraries.py [REQUIRED]"/>
27 <param name="method" type="text" value="fast" label="method"
28 help="Method to use for denoising. Choice of pyronoise or fast [default: fast]"/>
29 <param name="keep_intermediates" type="boolean" truevalue="--keep_intermediates" falsevalue="" checked="false" label="keep_intermediates"
30 help="Do not delete intermediate files -- useful for debugging [default: False]"/>
31 <param name="cut_off" type="float" value="0.05" label="cut-off"
32 help="cut-off value (passed to pyroNoise) [default: 0.05]"/>
33 <param name="precision" type="float" value="15.0" label="precision"
34 help="precision (passed to pyroNoise)[default: 15.0]"/>
35 <param name="num_cpus" type="integer" value="1" label="num_cpus"
36 help="number of CPUs [default: 1]"/>
37 <param name="force_overwrite" type="boolean" truevalue="--force_overwrite" falsevalue="" checked="false" label="force_overwrite"
38 help="Overwrite files in output directory [default: False]"/>
39 <param name="map_fname" type="data" format="tabular" label="map_fname"
40 help="name of mapping file, Has to contain field LinkerPrimerSequence. [REQUIRED] when method is fast"/>
41 <param name="primer" type="text" label="primer"
42 help="primer sequence [default: %default]"/>
43 </inputs>
44 <outputs>
45
46 </outputs>
47 <tests>
48 </tests>
49 <help>
50
51 </help>
52 </tool>
53