Mercurial > repos > jjohnson > qiime

annotate multiple_rarefactions.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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
1 <tool id="multiple_rarefactions" name="multiple_rarefactions" version="1.2.0">
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
2 <description>Perform multiple subsamplings/rarefactions on an otu table</description>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
3 <requirements>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
4 <requirement type="binary">multiple_rarefactions.py</requirement>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
5 </requirements>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
6 <command interpreter="python">
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
7 qiime_wrapper.py
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
8 --galaxy_tmpdir='$__new_file_path__'
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
9 multiple_rarefactions.py
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
10 --input_path=$input_path
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
11 --output_path=$output_path
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
12 --min=$min
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
13 --max=$max
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
14 --step=$step
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
15 --num-reps=$num_reps
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
16 $lineages_included
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
17 $keep_empty_otus
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
18 </command>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
19 <inputs>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
20 <param name="input_path" type="text" label="input_path"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
21 help="input otu table filepath [REQUIRED]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
22 <param name="min" type="integer" value="-1" label="min"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
23 help="min seqs/sample [REQUIRED]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
24 <param name="max" type="integer" value="-1" label="max"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
25 help="max seqs/sample (inclusive) [REQUIRED]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
26 <param name="step" type="integer" value="-1" label="step"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
27 help="levels: min, min+step... for level {= max [REQUIRED]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
28 <param name="num_reps" type="integer" value="1" label="num-reps"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
29 help="num iterations at each seqs/sample level [default: 1]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
30 <param name="lineages_included" type="boolean" truevalue="--lineages_included" falsevalue="" checked="false" label="lineages_included"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
31 help="output rarefied otu tables will include taxonomic (lineage) information for each otu, if present in input otu table [default: False]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
32 <param name="keep_empty_otus" type="boolean" truevalue="--keep_empty_otus" falsevalue="" checked="false" label="keep_empty_otus"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
33 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]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
34 </inputs>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
35 <outputs>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
36 <data format="txt" name="output_path"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
37 </outputs>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
38 <tests>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
39 </tests>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
40 <help>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
41
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
42 </help>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
43 </tool>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
44