Mercurial > repos > jjohnson > qiime
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 |
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| 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 |