Mercurial > repos > jjohnson > qiime

annotate sort_otu_table.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="sort_otu_table" name="sort_otu_table" version="1.2.1">
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
2 <description>Script for sorting the sample IDs in an OTU table based on a specified value in a mapping file.</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">sort_otu_table.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 sort_otu_table.py
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
9 --input_otu_table=$input_otu_table
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
10 --mapping_fp=$mapping_fp
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
11 --sort_field=$sort_field
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
12 --output_fp=$output_fp
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_otu_table" type="data" format="qiimeotu" label="input_otu_table"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
16 help="the input otu table [REQUIRED]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
17 <param name="mapping_fp" type="data" format="qiimemapping" label="mapping_fp"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
18 help="the mapping file [REQUIRED]"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
19 <param name="sort_field" type="select" label="sort_field"
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
20 help="field to sort by [REQUIRED]">
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
21 <options>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
22 <filter type="data_meta" ref="mapping_fp" key="column_names" />
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
23 </options>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
24 </param>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
25 </inputs>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
26 <outputs>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
27 <data format="txt" name="output_fp"/>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
28 </outputs>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
29 <tests>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
30 </tests>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
31 <help>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
32
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
33 </help>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
34 </tool>
e5c3175506b7 Initial tool configs for qiime, most need work.
Jim Johnson <jj@umn.edu>
parents:
diff changeset
35