Mercurial > repos > jjohnson > mothur_toolsuite
comparison 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 |
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date | Tue, 07 Jun 2011 17:39:06 -0400 |
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children | bfbaf823be4c |
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1 <tool id="mothur_get_otulist" name="Get.otulist" force_history_refresh="True" version="1.19.0"> | |
2 <description>Get otus for each distance in a otu list</description> | |
3 <command interpreter="python"> | |
4 mothur_wrapper.py | |
5 ## output {group_file_name}.pick.{label}.groups {list_file_name}.pick.{label}.list | |
6 #import re, os.path | |
7 --cmd='get.otulist' | |
8 --result='^mothur.\S+\.logfile$:'$logfile | |
9 --outputdir='$logfile.extra_files_path' | |
10 #if $as_datasets.__str__ == "yes": | |
11 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' | |
12 --new_datasets='^\S+?\.((unique|[0-9.]*)\.otu)$:tabular' | |
13 #end if | |
14 --list=$list_in | |
15 #if $label.__str__ != "None" and len($label.__str__) > 0: | |
16 --label=$label | |
17 #end if | |
18 #if $sort.__str__ != "None" and len($sort.__str__) > 0: | |
19 --sort=$sort | |
20 #end if | |
21 </command> | |
22 <inputs> | |
23 <param name="list_in" type="data" format="list" label="list - OTU List"/> | |
24 <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="By default, uses all if none are selected."> | |
25 <options from_dataset="list_in"> | |
26 <column name="name" index="0"/> | |
27 <column name="value" index="0"/> | |
28 </options> | |
29 </param> | |
30 <param name="sort" type="select" label="sort - select the output format"> | |
31 <help>If otu is selected the output will be otu number followed by the list of names in that otu. | |
32 If name is selected the output will be a sequence name followed by its otu number.</help> | |
33 <option value="otu" selected="true">otu</option> | |
34 <option value="name">name</option> | |
35 </param> | |
36 <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each label list"/> | |
37 </inputs> | |
38 <outputs> | |
39 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | |
40 </outputs> | |
41 <requirements> | |
42 <requirement type="binary">mothur</requirement> | |
43 </requirements> | |
44 <tests> | |
45 </tests> | |
46 <help> | |
47 **Mothur Overview** | |
48 | |
49 Mothur_, initiated by Dr. Patrick Schloss and his software development team | |
50 in the Department of Microbiology and Immunology at The University of Michigan, | |
51 provides bioinformatics for the microbial ecology community. | |
52 | |
53 .. _Mothur: http://www.mothur.org/wiki/Main_Page | |
54 | |
55 **Command Documenation** | |
56 | |
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. | |
58 | |
59 .. _get.otulist: http://www.mothur.org/wiki/Get.otulist | |
60 | |
61 | |
62 </help> | |
63 </tool> |