Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/get.groups.xml @ 24:09740be2bc9c
Mothur - updates for Mothur version 1.24
author | Jim Johnson <jj@umn.edu> |
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date | Wed, 28 Mar 2012 15:45:03 -0500 |
parents | 370b3fc4e7d3 |
children | bfbaf823be4c |
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23:efd36aa39261 | 24:09740be2bc9c |
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1 <tool id="mothur_get_groups" name="Get.groups" version="1.21.0"> | 1 <tool id="mothur_get_groups" name="Get.groups" version="1.24.0"> |
2 <description>Select groups</description> | 2 <description>Select groups</description> |
3 <command interpreter="python"> | 3 <command interpreter="python"> |
4 mothur_wrapper.py | 4 mothur_wrapper.py |
5 #import re, os.path | 5 #import re, os.path |
6 #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] | 6 #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] |
36 #end if | 36 #end if |
37 #if $taxonomy_in.__str__ != "None" and len($taxonomy_in.__str__) > 0: | 37 #if $taxonomy_in.__str__ != "None" and len($taxonomy_in.__str__) > 0: |
38 --taxonomy=$taxonomy_in | 38 --taxonomy=$taxonomy_in |
39 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($taxonomy_in.__str__)) + ":'" + $taxonomy_out.__str__] | 39 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($taxonomy_in.__str__)) + ":'" + $taxonomy_out.__str__] |
40 #end if | 40 #end if |
41 #if $design_in.__str__ != "None" and len($design_in.__str__) > 0: | |
42 --design=$design_in | |
43 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.*\\.pick\\.\2',$os.path.basename($design_in.__str__)) + ":'" + $design_out.__str__] | |
44 #end if | |
41 --result=#echo ','.join($results) | 45 --result=#echo ','.join($results) |
42 </command> | 46 </command> |
43 <inputs> | 47 <inputs> |
44 <param name="group_in" type="data" format="groups" label="group - Groups"/> | 48 <param name="group_in" type="data" format="groups" label="group - Groups"/> |
45 <conditional name="groupnames"> | 49 <conditional name="groupnames"> |
63 <param name="fasta_in" type="data" format="fasta,align" optional="true" label="fasta - Fasta Sequences"/> | 67 <param name="fasta_in" type="data" format="fasta,align" optional="true" label="fasta - Fasta Sequences"/> |
64 <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/> | 68 <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/> |
65 <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/> | 69 <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/> |
66 <param name="shared_in" type="data" format="shared" optional="true" label="shared - OTU Shared"/> | 70 <param name="shared_in" type="data" format="shared" optional="true" label="shared - OTU Shared"/> |
67 <param name="taxonomy_in" type="data" format="seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> | 71 <param name="taxonomy_in" type="data" format="seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> |
72 <param name="design_in" type="data" format="tabular" optional="true" label="design - assign groups to new grouping" | |
73 help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/> | |
68 </inputs> | 74 </inputs> |
69 <outputs> | 75 <outputs> |
70 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | 76 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
71 <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"/> | 77 <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"/> |
72 <!-- fix format --> | 78 <!-- fix format --> |
82 <data format="shared" name="shared_out" label="${tool.name} on ${on_string}: pick.shared"> | 88 <data format="shared" name="shared_out" label="${tool.name} on ${on_string}: pick.shared"> |
83 <filter>shared_in != None</filter> | 89 <filter>shared_in != None</filter> |
84 </data> | 90 </data> |
85 <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"> | 91 <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"> |
86 <filter>taxonomy_in != None</filter> | 92 <filter>taxonomy_in != None</filter> |
93 </data> | |
94 <data format="design" name="design_out" label="${tool.name} on ${on_string}: pick.design"> | |
95 <filter>design_in != None</filter> | |
87 </data> | 96 </data> |
88 </outputs> | 97 </outputs> |
89 <requirements> | 98 <requirements> |
90 <requirement type="binary">mothur</requirement> | 99 <requirement type="binary">mothur</requirement> |
91 </requirements> | 100 </requirements> |