Mercurial > repos > jjohnson > qiime
comparison multiple_rarefactions_even_depth.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="multiple_rarefactions_even_depth" name="multiple_rarefactions_even_depth" version="1.2.0"> | |
| 2 <description>Perform multiple rarefactions on a single otu table, at one depth of sequences/sample</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">multiple_rarefactions_even_depth.py</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 qiime_wrapper.py | |
| 8 --galaxy_tmpdir='$__new_file_path__' | |
| 9 multiple_rarefactions_even_depth.py | |
| 10 --input_path=$input_path | |
| 11 --output_path=$output_path | |
| 12 --depth=$depth | |
| 13 --num-reps=$num_reps | |
| 14 $lineages_included | |
| 15 $keep_empty_otus | |
| 16 </command> | |
| 17 <inputs> | |
| 18 <param name="input_path" type="text" label="input_path" | |
| 19 help="input otu table filepath [REQUIRED]"/> | |
| 20 <param name="depth" type="integer" value="-1" label="depth" | |
| 21 help="sequences per sample to subsample [REQUIRED]"/> | |
| 22 <param name="num_reps" type="integer" value="1" label="num-reps" | |
| 23 help="num iterations at each seqs/sample level [default: 1]"/> | |
| 24 <param name="lineages_included" type="boolean" truevalue="--lineages_included" falsevalue="" checked="false" label="lineages_included" | |
| 25 help="output rarefied otu tables will include taxonomic (lineage) information for each otu, if present in input otu table [default: False]"/> | |
| 26 <param name="keep_empty_otus" type="boolean" truevalue="--keep_empty_otus" falsevalue="" checked="false" label="keep_empty_otus" | |
| 27 help="otus (rows) of all zeros are usually omitted from the output otu tables, with -k they will not be removed from the output files [default: False]"/> | |
| 28 </inputs> | |
| 29 <outputs> | |
| 30 <data format="txt" name="output_path"/> | |
| 31 </outputs> | |
| 32 <tests> | |
| 33 </tests> | |
| 34 <help> | |
| 35 | |
| 36 </help> | |
| 37 </tool> | |
| 38 |