Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/remove.rare.xml @ 1:fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:35:35 -0400 |
parents | |
children | e990ac8a0f58 |
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0:3202a38e44d9 | 1:fcc0778f6987 |
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1 <tool id="mothur_remove_rare" name="Remove.rare" version="1.16.0"> | |
2 <description>Remove rare OTUs</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 #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] | |
8 --cmd='remove.rare' | |
9 --outputdir='$logfile.extra_files_path' | |
10 #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): | |
11 --shared=$otu | |
12 #if $group_in.__str__ != "None" and len($group_in.__str__) > 0: | |
13 --group=$group_in | |
14 #end if | |
15 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.otu_in.__str__)) + ":'" + $pick_shared.__str__] | |
16 #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__): | |
17 --rabund=$otu | |
18 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.otu_in.__str__)) + ":'" + $pick_rabund.__str__] | |
19 #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sabund').__class__): | |
20 --sabund=$otu | |
21 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.otu_in.__str__)) + ":'" + $pick_sabund.__str__] | |
22 #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__): | |
23 --list=$otu | |
24 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.otu_in.__str__)) + ":'" + $pick_list.__str__] | |
25 $bygroup | |
26 #end if | |
27 #if $label.__str__ != "None" and len($label.__str__) > 0: | |
28 --label=$label | |
29 #end if | |
30 #if $groups.__str__ != "None" and len($groups.__str__) > 0: | |
31 --groups=$groups | |
32 #end if | |
33 --nseqs=$nseqs | |
34 --result=#echo ','.join($results) | |
35 </command> | |
36 <inputs> | |
37 <param name="otu" type="data" format="list,rabund,sabund,shared" label="shared/relabund - Otu dataset"/> | |
38 <param name="group_in" type="data" format="groups" label="group - Groups" optional="true"/> | |
39 <param name="label" type="select" optional="true" label="label - OTU Labels" > | |
40 <options from_dataset="otu"> | |
41 <column name="name" index="0"/> | |
42 <column name="value" index="0"/> | |
43 <filter type="unique_value" name="unq_lbl" column="0" /> | |
44 </options> | |
45 </param> | |
46 <param name="groups" type="select" optional="true" label="groups - Pick groups to annalyze" multiple="true"> | |
47 <options from_dataset="otu"> | |
48 <column name="name" index="1"/> | |
49 <column name="value" index="1"/> | |
50 <filter type="unique_value" name="unq_grp" column="1" /> | |
51 </options> | |
52 </param> | |
53 <param name="nseqs" type="integer" value="1" label="nseqs - iNumber of sequences cutoff for an otu to be deemed rare"/> | |
54 <param name="bygroup" type="boolean" truevalue="--bygroup=true" falsevalue="" checked="false" label="bygroup - Remove any OTU that has nseqs or fewer sequences across all groups"/> | |
55 </inputs> | |
56 <outputs> | |
57 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | |
58 <data format="list" name="pick_list" label="${tool.name} on ${on_string}: pick.list"> | |
59 <filter>otu.datatype == 'list'</filter> | |
60 </data> | |
61 <data format="rabund" name="pick_rabund" label="${tool.name} on ${on_string}: pick.rabund"> | |
62 <filter>otu.datatype == 'rabund'</filter> | |
63 </data> | |
64 <data format="sabund" name="pick_sabund" label="${tool.name} on ${on_string}: pick.sabund"> | |
65 <filter>otu.datatype == 'sabund'</filter> | |
66 </data> | |
67 <data format="shared" name="pick_shared" label="${tool.name} on ${on_string}: pick.shared"> | |
68 <filter>otu.datatype == 'shared'</filter> | |
69 </data> | |
70 </outputs> | |
71 <requirements> | |
72 <requirement type="binary">mothur</requirement> | |
73 </requirements> | |
74 <tests> | |
75 </tests> | |
76 <help> | |
77 **Mothur Overview** | |
78 | |
79 Mothur_, initiated by Dr. Patrick Schloss and his software development team | |
80 in the Department of Microbiology and Immunology at The University of Michigan, | |
81 provides bioinformatics for the microbial ecology community. | |
82 | |
83 .. _Mothur: http://www.mothur.org/wiki/Main_Page | |
84 | |
85 **Command Documenation** | |
86 | |
87 The remove.rare_ command reads one of the following file types: list, rabund, sabund or shared file. It outputs a new file after removing the rare otus. | |
88 | |
89 .. _remove.rare: http://www.mothur.org/wiki/Remove.rare | |
90 | |
91 | |
92 </help> | |
93 </tool> |