Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/unique.seqs.xml @ 2:e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author | jjohnson |
---|---|
date | Tue, 07 Jun 2011 17:39:06 -0400 |
parents | fcc0778f6987 |
children | 5265aa9067e0 |
comparison
equal
deleted
inserted
replaced
1:fcc0778f6987 | 2:e990ac8a0f58 |
---|---|
1 <tool id="mothur_unique_seqs" name="Unique.seqs" version="1.16.0"> | 1 <tool id="mothur_unique_seqs" name="Unique.seqs" version="1.19.0"> |
2 <description>Return unique sequences</description> | 2 <description>Return unique sequences</description> |
3 <command interpreter="python"> | 3 <command interpreter="python"> |
4 mothur_wrapper.py | 4 mothur_wrapper.py |
5 --cmd='unique.seqs' | 5 --cmd='unique.seqs' |
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.unique\.\w+$:'$out_fasta,'^\S+\.names$:'$out_names | 6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.unique\.\w+$:'$out_fasta,'^\S+\.names$:'$out_names |
7 --outputdir='$logfile.extra_files_path' | 7 --outputdir='$logfile.extra_files_path' |
8 --fasta=$fasta | 8 --fasta=$fasta |
9 --name=$names | 9 #if $names.__str__ != "None" and len($names.__str__) > 0: |
10 --name=$names | |
11 #end if | |
10 </command> | 12 </command> |
11 <inputs> | 13 <inputs> |
12 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/> | 14 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/> |
13 <param name="names" type="data" format="names" optional="true" label="names - Sequences Names"/> | 15 <param name="names" type="data" format="names" optional="true" label="names - Sequences Names"/> |
14 </inputs> | 16 </inputs> |
31 | 33 |
32 .. _Mothur: http://www.mothur.org/wiki/Main_Page | 34 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
33 | 35 |
34 **Command Documenation** | 36 **Command Documenation** |
35 | 37 |
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. | 38 The unique.seqs_ command returns only the unique sequences found in a fasta-formatted sequence file and a name_ file that indicates those sequences that are identical to the reference sequence. |
37 | 39 |
40 .. _name: http://www.mothur.org/wiki/Name_file | |
38 .. _unique.seqs: http://www.mothur.org/wiki/Unique.seqs | 41 .. _unique.seqs: http://www.mothur.org/wiki/Unique.seqs |
39 | 42 |
40 | 43 |
41 </help> | 44 </help> |
42 </tool> | 45 </tool> |