Mercurial > repos > jjohnson > qiime
comparison make_otu_table.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="make_otu_table" name="make_otu_table" version="1.2.0"> | |
| 2 <description>Make OTU table</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">make_otu_table.py</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 qiime_wrapper.py | |
| 8 make_otu_table.py | |
| 9 --otu_map_fp=$otu_map_fp | |
| 10 --taxonomy=$taxonomy | |
| 11 --exclude_otus_fp=$exclude_otus_fp | |
| 12 --output_fp=$output_fp | |
| 13 </command> | |
| 14 <inputs> | |
| 15 <param name="otu_map_fp" type="data" format="qiimeotu" label="otu_map_fp" | |
| 16 help="path to the input OTU map (i.e., the output from pick_otus.py) [REQUIRED]"/> | |
| 17 <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy" | |
| 18 help="Path to taxonomy assignment, containing the assignments of \ taxons to sequences (i.e., resulting txt file from assign_taxonomy.py) [default: %default]"/> | |
| 19 <param name="exclude_otus_fp" type="data" format="txt" label="exclude_otus_fp" | |
| 20 help="a filepath listing OTU identifiers that should not be included in the OTU table (e.g., the output of identify_chimeric_seqs.py)"/> | |
| 21 </inputs> | |
| 22 <outputs> | |
| 23 <data format="qiimeotutable" name="output_fp" label="${tool.name} on ${on_string}: otu_table"/> | |
| 24 </outputs> | |
| 25 <tests> | |
| 26 </tests> | |
| 27 <help> | |
| 28 | |
| 29 </help> | |
| 30 </tool> | |
| 31 |