Mercurial > repos > jjohnson > qiime
comparison filter_otus_by_sample.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="filter_otus_by_sample" name="filter_otus_by_sample" version="1.2.0"> | |
2 <description>Filter OTU mapping file and sequences by SampleIDs</description> | |
3 <requirements> | |
4 <requirement type="binary">filter_otus_by_sample.py</requirement> | |
5 </requirements> | |
6 <command interpreter="python"> | |
7 qiime_wrapper.py | |
8 --galaxy_tmpdir='$__new_file_path__' | |
9 filter_otus_by_sample.py | |
10 --otu_map_fp=$otu_map_fp | |
11 --input_fasta_fp=$input_fasta_fp | |
12 --samples_to_extract=$samples_to_extract | |
13 --output_dir=$__new_file_path__ | |
14 </command> | |
15 <inputs> | |
16 <param name="otu_map_fp" type="data" format="tabular" label="otu_map_fp" | |
17 help="path to the input OTU map (i.e., the output from pick_otus.py) [REQUIRED]"/> | |
18 <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp" | |
19 help="path to the input fasta file [REQUIRED]"/> | |
20 <param name="samples_to_extract" type="text" label="samples_to_extract" | |
21 help="This is a list of sample ids, which should be removed from the OTU file [REQUIRED]"/> | |
22 </inputs> | |
23 <outputs> | |
24 | |
25 </outputs> | |
26 <tests> | |
27 </tests> | |
28 <help> | |
29 | |
30 </help> | |
31 </tool> | |
32 |