Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/get.otulist.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 | |
children | bfbaf823be4c |
rev | line source |
---|---|
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1 <tool id="mothur_get_otulist" name="Get.otulist" force_history_refresh="True" version="1.19.0"> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
2 <description>Get otus for each distance in a otu list</description> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
3 <command interpreter="python"> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
4 mothur_wrapper.py |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
5 ## output {group_file_name}.pick.{label}.groups {list_file_name}.pick.{label}.list |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
6 #import re, os.path |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
7 --cmd='get.otulist' |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
8 --result='^mothur.\S+\.logfile$:'$logfile |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
9 --outputdir='$logfile.extra_files_path' |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
10 #if $as_datasets.__str__ == "yes": |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
11 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
12 --new_datasets='^\S+?\.((unique|[0-9.]*)\.otu)$:tabular' |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
13 #end if |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
14 --list=$list_in |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
15 #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:
diff
changeset
|
16 --label=$label |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
17 #end if |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
18 #if $sort.__str__ != "None" and len($sort.__str__) > 0: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
19 --sort=$sort |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
20 #end if |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
21 </command> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
22 <inputs> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
23 <param name="list_in" type="data" format="list" label="list - OTU List"/> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
24 <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="By default, uses all if none are selected."> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
25 <options from_dataset="list_in"> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
26 <column name="name" index="0"/> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
27 <column name="value" index="0"/> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
28 </options> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
29 </param> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
30 <param name="sort" type="select" label="sort - select the output format"> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
31 <help>If otu is selected the output will be otu number followed by the list of names in that otu. |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
32 If name is selected the output will be a sequence name followed by its otu number.</help> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
33 <option value="otu" selected="true">otu</option> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
34 <option value="name">name</option> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
35 </param> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
36 <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each label list"/> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
37 </inputs> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
38 <outputs> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
39 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
40 </outputs> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
41 <requirements> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
42 <requirement type="binary">mothur</requirement> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
43 </requirements> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
44 <tests> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
45 </tests> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
46 <help> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
47 **Mothur Overview** |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
48 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
49 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
50 in the Department of Microbiology and Immunology at The University of Michigan, |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
51 provides bioinformatics for the microbial ecology community. |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
52 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
53 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
54 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
55 **Command Documenation** |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
56 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
57 The get.otulist_ command parses a list file and creates an .otu file for each distance containing 2 columns. The first column is the OTU number the second column is a list of sequences in that OTU. |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
58 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
59 .. _get.otulist: http://www.mothur.org/wiki/Get.otulist |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
60 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
61 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
62 </help> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
63 </tool> |