Mercurial > repos > jjohnson > qiime

comparison single_rarefaction.xml @ 0:e5c3175506b7 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:e5c3175506b7
1 <tool id="single_rarefaction" name="single_rarefaction" version="1.2.0">
2 <description>Perform rarefaction on an otu table</description>
3 <requirements>
4 <requirement type="binary">single_rarefaction.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 single_rarefaction.py
9 --input_path=$input_path
10 --output_path=$output_path
11 --depth=$depth
12 $lineages_included
13 $keep_empty_otus
14 </command>
15 <inputs>
16 <param name="input_path" type="qiimeotutable" label="input_path"
17 help="input otu table filepath [REQUIRED]"/>
18 <param name="depth" type="integer" value="-1" label="depth"
19 help="sequences per sample to subsample [REQUIRED]"/>
20 <param name="lineages_included" type="boolean" truevalue="--lineages_included" falsevalue="" checked="false" label="lineages_included"
21 help="output rarefied otu tables will include taxonomic (lineage) information for each otu, if present in input otu table [default: False]"/>
22 <param name="keep_empty_otus" type="boolean" truevalue="--keep_empty_otus" falsevalue="" checked="false" label="keep_empty_otus"
23 help="otus (rows) of all zeros are usually omitted from the output otu table, with -k they will not be removed from the output file [default: False]"/>
24 </inputs>
25 <outputs>
26 <data format_source="input_path" name="output_path" label="${tool.name} on ${on_string}: rarefaction"/>
27 </outputs>
28 <tests>
29 </tests>
30 <help>
31
32 </help>
33 </tool>
34