Mercurial > repos > jjohnson > qiime
comparison summarize_taxa.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="summarize_taxa" name="summarize_taxa" version="1.2.1"> | |
| 2 <description>Summarize Taxa</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">summarize_taxa.py</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 qiime_wrapper.py | |
| 8 summarize_taxa.py | |
| 9 --otu_table_fp=$otu_table_fp | |
| 10 --output_fp=$output_fp | |
| 11 --level=$level | |
| 12 #if $mapping != None and $mapping.__str__ != 'None': | |
| 13 --mapping=$mapping | |
| 14 #end if | |
| 15 #if $delimiter != ';': | |
| 16 --delimiter=$delimiter | |
| 17 #end if | |
| 18 ## --relative_abundance=$relative_abundance | |
| 19 $absolute_abundance | |
| 20 </command> | |
| 21 <inputs> | |
| 22 <param name="otu_table_fp" type="data" format="qiimeotutable" label="otu_table_fp" | |
| 23 help="Path to read otu file [REQUIRED]"/> | |
| 24 <param name="level" type="integer" value="2" label="level" | |
| 25 help="Level of taxonomy to use [default: 2]"/> | |
| 26 <param name="mapping" type="data" format="qiimemapping" optional="true" label="mapping" | |
| 27 help="if supplied - the taxon information will be added to the mapping file. This mapping file can be used to color PCoA plots by taxon abundance or to perform statistical tests of taxon/mappingy associations."/> | |
| 28 <param name="delimiter" type="text" value="\;" label="delimiter" | |
| 29 help="Delimitor that separates taxonomy categories.[default: ;]"/> | |
| 30 <param name="absolute_abundance" type="boolean" truevalue="--absolute_abundance" falsevalue="" checked="false" label="absolute_abundance" | |
| 31 help="If present, reports the absolute abundance of the lineage in each sample. By default uses relative abundance [default: False]"/> | |
| 32 </inputs> | |
| 33 <outputs> | |
| 34 <data format="qiimetaxsummary" name="output_fp" label="${tool.name} on ${on_string}: taxa_summary"/> | |
| 35 </outputs> | |
| 36 <tests> | |
| 37 </tests> | |
| 38 <help> | |
| 39 | |
| 40 </help> | |
| 41 </tool> | |
| 42 |