Mercurial > repos > jjohnson > qiime

annotate consensus_tree.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="consensus_tree" name="consensus_tree" version="1.2.0">
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
2 <description>This script outputs a majority consensus tree given a collection of input trees.</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">consensus_tree.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='$__new_file_path__'
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
9 consensus_tree.py
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
10 --input_dir=$input_dir
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
11 --output_fname=$output_fname
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
12 $strict
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
13 </command>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
14 <inputs>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
15 <param name="input_dir" type="text" label="input_dir"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
16 help="input folder containing trees [REQUIRED]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
17 <param name="strict" type="boolean" truevalue="--strict" falsevalue="" checked="false" label="strict"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
18 help="Use only nodes occurring }50% of the time [default: False]"/>
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 <outputs>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
21 <data format="txt" name="output_fname"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
22 </outputs>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
23 <tests>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
24 </tests>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
25 <help>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
26
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
27 </help>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
28 </tool>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
29