Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/remove.rare.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 |
parents | fcc0778f6987 |
children | 7bfe1f843858 |
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1:fcc0778f6987 | 2:e990ac8a0f58 |
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1 <tool id="mothur_remove_rare" name="Remove.rare" version="1.16.0"> | 1 <tool id="mothur_remove_rare" name="Remove.rare" version="1.19.0"> |
2 <description>Remove rare OTUs</description> | 2 <description>Remove rare OTUs</description> |
3 <command interpreter="python"> | 3 <command interpreter="python"> |
4 mothur_wrapper.py | 4 mothur_wrapper.py |
5 ## output {group_file_name}.pick.{label}.groups {list_file_name}.pick.{label}.list | 5 ## output {group_file_name}.pick.groups {list_file_name}.pick.{format} |
6 #import re, os.path | 6 #import re, os.path |
7 #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] | 7 #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] |
8 --cmd='remove.rare' | 8 --cmd='remove.rare' |
9 --outputdir='$logfile.extra_files_path' | 9 --outputdir='$logfile.extra_files_path' |
10 #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): | 10 #if isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): |
11 --shared=$otu | 11 --shared=$input.otu |
12 #if $group_in.__str__ != "None" and len($group_in.__str__) > 0: | 12 $input.bygroup |
13 --group=$group_in | 13 #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: |
14 --groups=$input.groups | |
14 #end if | 15 #end if |
15 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.otu_in.__str__)) + ":'" + $pick_shared.__str__] | 16 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.otu.__str__)) + ":'" + $pick_otu.__str__] |
16 #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__): | 17 #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__): |
17 --rabund=$otu | 18 --rabund=$input.otu |
18 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.otu_in.__str__)) + ":'" + $pick_rabund.__str__] | 19 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.otu.__str__)) + ":'" + $pick_otu.__str__] |
19 #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sabund').__class__): | 20 #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sabund').__class__): |
20 --sabund=$otu | 21 --sabund=$input.otu |
21 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.otu_in.__str__)) + ":'" + $pick_sabund.__str__] | 22 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.otu.__str__)) + ":'" + $pick_otu.__str__] |
22 #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__): | 23 #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__): |
23 --list=$otu | 24 --list=$input.otu |
24 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.otu_in.__str__)) + ":'" + $pick_list.__str__] | 25 #if $input.group.__str__ != "None" and len($input.group.__str__) > 0: |
25 $bygroup | 26 --group=$input.group |
27 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.group.__str__)) + ":'" + $pick_group.__str__] | |
28 #end if | |
29 #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: | |
30 --groups=$input.groups | |
31 #end if | |
32 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($input.otu.__str__)) + ":'" + $pick_otu.__str__] | |
26 #end if | 33 #end if |
27 #if $label.__str__ != "None" and len($label.__str__) > 0: | 34 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: |
28 --label=$label | 35 --label=$input.label |
29 #end if | |
30 #if $groups.__str__ != "None" and len($groups.__str__) > 0: | |
31 --groups=$groups | |
32 #end if | 36 #end if |
33 --nseqs=$nseqs | 37 --nseqs=$nseqs |
34 --result=#echo ','.join($results) | 38 --result=#echo ','.join($results) |
35 </command> | 39 </command> |
36 <inputs> | 40 <inputs> |
37 <param name="otu" type="data" format="list,rabund,sabund,shared" label="shared/relabund - Otu dataset"/> | 41 <conditional name="input"> |
38 <param name="group_in" type="data" format="groups" label="group - Groups" optional="true"/> | 42 <param name="source" type="select" label="Select Input Format"> |
39 <param name="label" type="select" optional="true" label="label - OTU Labels" > | 43 <option value="shared">shared</option> |
40 <options from_dataset="otu"> | 44 <option value="list">list and groups</option> |
41 <column name="name" index="0"/> | 45 <option value="default">rabund, sabund, or list</option> |
42 <column name="value" index="0"/> | 46 </param> |
43 <filter type="unique_value" name="unq_lbl" column="0" /> | 47 <when value="shared"> |
44 </options> | 48 <param name="otu" type="data" format="shared" label="shared - Otu dataset"/> |
45 </param> | 49 <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true"> |
46 <param name="groups" type="select" optional="true" label="groups - Pick groups to annalyze" multiple="true"> | 50 <options from_dataset="otu"> |
47 <options from_dataset="otu"> | 51 <column name="name" index="1"/> |
48 <column name="name" index="1"/> | 52 <column name="value" index="1"/> |
49 <column name="value" index="1"/> | 53 <filter type="unique_value" name="unq_grp" column="1" /> |
50 <filter type="unique_value" name="unq_grp" column="1" /> | 54 </options> |
51 </options> | 55 </param> |
52 </param> | 56 <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"/> |
53 <param name="nseqs" type="integer" value="1" label="nseqs - iNumber of sequences cutoff for an otu to be deemed rare"/> | 57 <param name="label" type="select" multiple="true" optional="true" label="label - OTU Labels" > |
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"/> | 58 <options from_dataset="otu"> |
59 <column name="name" index="0"/> | |
60 <column name="value" index="0"/> | |
61 <filter type="unique_value" name="unq_lbl" column="0" /> | |
62 </options> | |
63 </param> | |
64 </when> | |
65 <when value="list"> | |
66 <param name="otu" type="data" format="list" label="list - Otu dataset"/> | |
67 <param name="group" type="data" format="groups" label="group - Groups" /> | |
68 <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true"> | |
69 <options from_dataset="group"> | |
70 <column name="name" index="1"/> | |
71 <column name="value" index="1"/> | |
72 <filter type="unique_value" name="unq_grp" column="1" /> | |
73 </options> | |
74 </param> | |
75 <param name="label" type="select" multiple="false" optional="true" label="label - OTU Labels" > | |
76 <options from_dataset="otu"> | |
77 <column name="name" index="0"/> | |
78 <column name="value" index="0"/> | |
79 <filter type="unique_value" name="unq_lbl" column="0" /> | |
80 </options> | |
81 </param> | |
82 </when> | |
83 <when value="default"> | |
84 <param name="otu" type="data" format="shared,list,rabund,sabund" label="shared,list,rabund,sabund - Otu dataset"/> | |
85 <param name="label" type="select" multiple="true" optional="true" label="label - OTU Labels" > | |
86 <options from_dataset="otu"> | |
87 <column name="name" index="0"/> | |
88 <column name="value" index="0"/> | |
89 <filter type="unique_value" name="unq_lbl" column="0" /> | |
90 </options> | |
91 </param> | |
92 </when> | |
93 </conditional> | |
94 <param name="nseqs" type="integer" value="1" label="nseqs - Number of sequences cutoff for an otu to be deemed rare"/> | |
55 </inputs> | 95 </inputs> |
56 <outputs> | 96 <outputs> |
57 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | 97 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
58 <data format="list" name="pick_list" label="${tool.name} on ${on_string}: pick.list"> | 98 <data format_source="otu" name="pick_otu" label="${tool.name} on ${on_string}: pick.${input.otu.ext}"/> |
59 <filter>otu.datatype == 'list'</filter> | 99 <data format="groups" name="pick_group" label="${tool.name} on ${on_string}: pick.groups"> |
60 </data> | 100 <filter>input['source'] == 'list'</filter> |
61 <data format="rabund" name="pick_rabund" label="${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> | 101 </data> |
70 </outputs> | 102 </outputs> |
71 <requirements> | 103 <requirements> |
72 <requirement type="binary">mothur</requirement> | 104 <requirement type="binary">mothur</requirement> |
73 </requirements> | 105 </requirements> |
82 | 114 |
83 .. _Mothur: http://www.mothur.org/wiki/Main_Page | 115 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
84 | 116 |
85 **Command Documenation** | 117 **Command Documenation** |
86 | 118 |
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. | 119 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 | 120 |
121 .. _list: http://www.mothur.org/wiki/List_file | |
122 .. _sabund: http://www.mothur.org/wiki/Sabund_file | |
123 .. _rabund: http://www.mothur.org/wiki/Rabund_file | |
124 .. _shared: http://www.mothur.org/wiki/Shared_file | |
89 .. _remove.rare: http://www.mothur.org/wiki/Remove.rare | 125 .. _remove.rare: http://www.mothur.org/wiki/Remove.rare |
90 | 126 |
91 | 127 |
92 </help> | 128 </help> |
93 </tool> | 129 </tool> |