Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/bin.seqs.xml @ 33:d53b9eb16c2d
mothur_wrapper.py - convert_value needs to return a String
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Wed, 11 Sep 2013 16:56:31 -0500 |
parents | 49058b1f8d3f |
children | 95d75b35e4d2 |
rev | line source |
---|---|
7 | 1 <tool id="mothur_bin_seqs" name="Bin.seqs" version="1.20.0" force_history_refresh="True"> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
2 <description>Order Sequences by OTU</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='bin.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 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
7 --outputdir='$logfile.extra_files_path' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
8 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' |
4 | 9 --new_datasets='^\S+?\.(unique|[0-9.]*)\.fasta$:${fasta.ext}' |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
10 --fasta=$fasta |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
11 --list=$otu |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
12 #if $name.__str__ != "None" and len($name.__str__) > 0: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
13 --name=$name |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
14 #end if |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
15 #if $label.__str__ != "None" and len($label.__str__) > 0: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
16 --label='$label' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
17 #end if |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
18 #if $group.__str__ != "None" and len($group.__str__) > 0: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
19 --group='$group' |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
20 #end if |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
21 </command> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
22 <inputs> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
23 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin"/> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
24 <param name="otu" type="data" format="list" label="list - OTU List"/> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
25 <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
26 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
25
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
27 <options> |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
28 <filter type="data_meta" ref="otu" key="labels" /> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
29 </options> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
30 </param> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
31 <param name="group" type="data" format="group" optional="true" label="group - Sequences Name reference"/> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
32 </inputs> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
33 <outputs> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
34 <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
|
35 </outputs> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
36 <requirements> |
27
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
37 <requirement type="package" version="1.27">mothur</requirement> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
38 </requirements> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
39 <tests> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
40 </tests> |
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 **Mothur Overview** |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
43 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
44 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
|
45 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
|
46 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
|
47 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
48 .. _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
|
49 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
50 **Command Documenation** |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
51 |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
52 The bin.seqs_ command generates fasta-formatted files where sequences are ordered according to the OTU from the list_file_ that they belong to. Such an output may be helpful for generating primers specific to an OTU or for classification of sequences. |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
53 |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
54 .. _list_file: http://www.mothur.org/wiki/List_file |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
55 .. _bin.seqs: http://www.mothur.org/wiki/Bin.seqs |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
56 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
57 </help> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
58 </tool> |