Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/get.relabund.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_get_relabund" name="Get.relabund" version="1.20.0"> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
2 <description>Calculate the relative abundance of each 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='get.relabund' |
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+\.relabund$:'$relabund |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
7 --outputdir='$logfile.extra_files_path' |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
8 --shared=$otu |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
9 #if $label.__str__ != "None" and len($label.__str__) > 0: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
10 --label='$label' |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
11 #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
|
12 #if $groups.__str__ != "None" and len($groups.__str__) > 0: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
13 --groups=$groups |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
0
diff
changeset
|
14 #end if |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
15 #if $scale.__str__ != "None" and len($scale.__str__) > 0: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
16 --scale=$scale |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
17 #end if |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
18 </command> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
19 <inputs> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
20 <param name="otu" type="data" format="shared" label="shared - OTU Shared" |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
21 help="Use Make.shared to create a shared file from a list and a group file"/> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
22 <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
|
23 <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
|
24 <filter type="data_meta" ref="otu" key="labels" /> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
25 </options> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
26 </param> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
27 <param name="groups" type="select" label="groups - Groups to consider" 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
|
28 <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
|
29 <filter type="data_meta" ref="otu" key="groups" /> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
30 </options> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
31 </param> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
32 <param name="scale" type="select" label="scale - Scale by"> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
33 <option value="">Use default</option> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
34 <option value="totalgroup" selected="true">Total Groups</option> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
35 <option value="totalotu">Total OTUs</option> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
36 <option value="averagegroup">Average Groups</option> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
37 <option value="averageotu">Average OTUs</option> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
38 </param> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
39 </inputs> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
40 <outputs> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
41 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
42 <data format="relabund" name="relabund" label="${tool.name} on ${on_string}: relabund" /> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
43 </outputs> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
44 <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
|
45 <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
|
46 </requirements> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
47 <tests> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
48 </tests> |
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 **Mothur Overview** |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
51 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
52 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
|
53 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
|
54 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
|
55 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
56 .. _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
|
57 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
58 **Command Documenation** |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
59 |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
60 The get.relabund_ command calculates the relative abundance of each otu in a sample from a shared_ file. It outputs a .relabund_ file. |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
61 |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
62 .. _shared: http://www.mothur.org/wiki/Shared_file |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
63 .. _get.relabund: http://www.mothur.org/wiki/Get.relabund |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
64 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
65 </help> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
66 </tool> |