Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/remove.otus.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 | 370b3fc4e7d3 |
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1:fcc0778f6987 | 2:e990ac8a0f58 |
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1 <tool id="mothur_remove_otus" name="Remove.otus" version="1.16.0"> | 1 <tool id="mothur_remove_otus" name="Remove.otus" version="1.19.0"> |
2 <description>Remove otus containing sequences from specified groups</description> | 2 <description>Remove otus containing sequences from specified groups</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.{label}.groups {list_file_name}.pick.{label}.list |
6 #import re, os.path | 6 #import re, os.path |
7 --cmd='remove.otus' | 7 --cmd='remove.otus' |
8 --outputdir='$logfile.extra_files_path' | 8 --outputdir='$logfile.extra_files_path' |
9 --group=$group_in | 9 --group=$group_in |
10 --list=$list_in | 10 --list=$list_in |
11 --label=$label | 11 --label=$label |
12 #if $groups.__str__ != "None" and len($groups.__str__) > 0: | 12 #if $groupnames.source == 'groups': |
13 --groups=$groups | 13 #if $groupnames.groups.__str__ != "None" and len($groupnames.groups.__str__) > 0: |
14 #end if | 14 --groups=$groupnames.groups |
15 #if $accnos.__str__ != "None" and len($accnos.__str__) > 0: | 15 #end if |
16 --accnos=$accnos | 16 #else |
17 #if $groupnames.accnos.__str__ != "None" and len($groupnames.accnos.__str__) > 0: | |
18 --accnos=$groupnames.accnos | |
19 #end if | |
17 #end if | 20 #end if |
18 #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] | 21 #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] |
19 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.' + $label.__str__ + '.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__] | 22 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.' + $label.__str__ + '.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__] |
20 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.'+ $label.__str__ + '.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__] | 23 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.'+ $label.__str__ + '.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__] |
21 --result=#echo ','.join($results) | 24 --result=#echo ','.join($results) |
27 <options from_dataset="list_in"> | 30 <options from_dataset="list_in"> |
28 <column name="name" index="0"/> | 31 <column name="name" index="0"/> |
29 <column name="value" index="0"/> | 32 <column name="value" index="0"/> |
30 </options> | 33 </options> |
31 </param> | 34 </param> |
32 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true"> | 35 <conditional name="groupnames"> |
33 <options from_dataset="group_in"> | 36 <param name="source" type="select" label="Select Group Names from"> |
34 <column name="name" index="1"/> | 37 <option value="groups">A List of Group Names</option> |
35 <column name="value" index="1"/> | 38 <option value="accnos">A History Group Name Accnos Dataset</option> |
36 <filter type="unique_value" name="unq_grp" column="1" /> | 39 </param> |
37 </options> | 40 <when value="groups"> |
38 </param> | 41 <param name="groups" type="select" label="groups - Pick groups to include" multiple="true" force_select="true"> |
39 <param name="accnos" type="data" format="accnos" optional="true" label="accnos - Group Names from your history"/> | 42 <help>At least one group must be selected</help> |
43 <options from_dataset="group_in"> | |
44 <column name="name" index="1"/> | |
45 <column name="value" index="1"/> | |
46 <filter type="unique_value" name="unq_grp" column="1" /> | |
47 </options> | |
48 </param> | |
49 </when> | |
50 <when value="accnos"> | |
51 <param name="accnos" type="data" format="accnos" optional="true" label="accnos - Group Names from your history"/> | |
52 </when> | |
53 </conditional> | |
40 </inputs> | 54 </inputs> |
41 <outputs> | 55 <outputs> |
42 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | 56 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
43 <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"/> | 57 <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"/> |
44 <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"/> | 58 <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"/> |
57 | 71 |
58 .. _Mothur: http://www.mothur.org/wiki/Main_Page | 72 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
59 | 73 |
60 **Command Documenation** | 74 **Command Documenation** |
61 | 75 |
62 The remove.otus_ command removes otus containing sequences from a specific group or set of groups. | 76 The remove.otus_ command removes otus from a list_ containing sequences from a specific group or set of groups. |
63 | 77 |
78 .. _list: http://www.mothur.org/wiki/List_file | |
64 .. _remove.otus: http://www.mothur.org/wiki/Remove.otus | 79 .. _remove.otus: http://www.mothur.org/wiki/Remove.otus |
65 | 80 |
66 | 81 |
67 </help> | 82 </help> |
68 </tool> | 83 </tool> |