Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/chop.seqs.xml @ 15:a6189f58fedb
Mothur - updated for Mothur version 1.22.0
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Tue, 08 Nov 2011 11:45:32 -0600 |
parents | e990ac8a0f58 |
children | 49058b1f8d3f |
rev | line source |
---|---|
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
1 <tool id="mothur_chop_seqs" name="Chop.seqs" version="1.19.0"> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
2 <description>Trim sequences to a specified length</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='chop.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+.chop\.fasta$:'$out_fasta |
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 --numbases=$numbases |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
10 --keep=$keep |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
11 $countgaps |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
12 $short |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
13 </command> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
14 <inputs> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
15 <param name="fasta" type="data" format="fasta,align" label="fasta - Sequences to be chopped"/> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
16 <param name="numbases" type="integer" value="10" label="numbases - Number of bases to keep"/> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
17 <param name="keep" type="select" label="keep - Part of the sequence to keep"> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
18 <option value="front">front</option> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
19 <option value="back">back</option> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
20 </param> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
21 <param name="countgaps" type="boolean" truevalue="--countgaps=true" falsevalue="" checked="false" label="countgaps - Count gaps as bases"/> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
22 <param name="short" type="boolean" truevalue="--short=true" falsevalue="" checked="false" label="short - keep sequences that are too short to chop"/> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
23 </inputs> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
24 <outputs> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
25 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
26 <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: chop.fasta" /> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
27 </outputs> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
28 <requirements> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
29 <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
|
30 </requirements> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
31 <tests> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
32 </tests> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
33 <help> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
34 **Mothur Overview** |
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 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
|
37 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
|
38 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
|
39 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
40 .. _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
|
41 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
42 **Command Documenation** |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
43 |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
44 The chop.seqs_ command reads a fasta file of sequences and outputs a .chop.fasta file containing the trimmed sequences. It works on both aligned and unaligned sequences. |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
45 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
46 .. _chop.seqs: http://www.mothur.org/wiki/Chop.seqs |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
47 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
48 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
49 </help> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
50 </tool> |