Mercurial > repos > jjohnson > mothur_toolsuite

annotate mothur/tools/mothur/unique.seqs.xml @ 1:fcc0778f6987

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
author jjohnson
date Tue, 07 Jun 2011 17:35:35 -0400
parents 3202a38e44d9
children e990ac8a0f58
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
fcc0778f6987 Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 0
diff changeset
1 <tool id="mothur_unique_seqs" name="Unique.seqs" version="1.16.0">
0
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
2 <description>Return unique sequences</description>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
3 <command interpreter="python">
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
4 mothur_wrapper.py
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
5 --cmd='unique.seqs'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.unique\.\w+$:'$out_fasta,'^\S+\.names$:'$out_names
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
7 --outputdir='$logfile.extra_files_path'
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
8 --fasta=$fasta
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
9 --name=$names
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
10 </command>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
11 <inputs>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
12 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
13 <param name="names" type="data" format="names" optional="true" label="names - Sequences Names"/>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
14 </inputs>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
15 <outputs>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
16 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
17 <data format="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" />
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
18 <data format="names" name="out_names" label="${tool.name} on ${on_string}: names" />
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
19 </outputs>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
20 <requirements>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
21 <requirement type="binary">mothur</requirement>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
22 </requirements>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
23 <tests>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
24 </tests>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
25 <help>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
26 **Mothur Overview**
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
27
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
28 Mothur_, initiated by Dr. Patrick Schloss and his software development team
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
29 in the Department of Microbiology and Immunology at The University of Michigan,
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
30 provides bioinformatics for the microbial ecology community.
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
31
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
32 .. _Mothur: http://www.mothur.org/wiki/Main_Page
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
33
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
34 **Command Documenation**
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
35
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
36 The unique.seqs_ command returns only the unique sequences found in a fasta-formatted sequence file and a file that indicates those sequences that are identical to the reference sequence.
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
37
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
38 .. _unique.seqs: http://www.mothur.org/wiki/Unique.seqs
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
39
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
40
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
41 </help>
3202a38e44d9 Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
42 </tool>