Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/get.groups.xml @ 12:370b3fc4e7d3
Mothur galaxy tool updates for Mothur version 1.21.0, fix help section warnings
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Tue, 09 Aug 2011 11:39:27 -0500 |
| parents | 7bfe1f843858 |
| children | 09740be2bc9c |
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| 11:11867a45a43d | 12:370b3fc4e7d3 |
|---|---|
| 1 <tool id="mothur_get_groups" name="Get.groups" version="1.20.0"> | 1 <tool id="mothur_get_groups" name="Get.groups" version="1.21.0"> |
| 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__] |
| 7 ## adds .pick before the last extension to the input file | 7 ## adds .pick before the last extension to the input file |
| 8 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__] | 8 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__] |
| 9 --cmd='get.groups' | 9 --cmd='get.groups' |
| 10 --outputdir='$logfile.extra_files_path' | 10 --outputdir='$logfile.extra_files_path' |
| 11 --group=$group_in | 11 --group=$group_in |
| 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 #if $fasta_in.__str__ != "None" and len($fasta_in.__str__) > 0: | 21 #if $fasta_in.__str__ != "None" and len($fasta_in.__str__) > 0: |
| 19 --fasta=$fasta_in | 22 --fasta=$fasta_in |
| 20 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($fasta_in.__str__)) + ":'" + $fasta_out.__str__] | 23 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($fasta_in.__str__)) + ":'" + $fasta_out.__str__] |
| 21 #end if | 24 #end if |
| 22 #if $name_in.__str__ != "None" and len($name_in.__str__) > 0: | 25 #if $name_in.__str__ != "None" and len($name_in.__str__) > 0: |
| 23 --name=$name_in | 26 --name=$name_in |
| 24 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__] | 27 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__] |
| 25 #end if | 28 #end if |
| 26 #if $list_in.__str__ != "None" and len($list_in.__str__) > 0: | 29 #if $list_in.__str__ != "None" and len($list_in.__str__) > 0: |
| 27 --list=$list_in | 30 --list=$list_in |
| 28 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__] | 31 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__] |
| 32 #end if | |
| 33 #if $shared_in.__str__ != "None" and len($shared_in.__str__) > 0: | |
| 34 --shared=$shared_in | |
| 35 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.*\\.pick\\.\2',$os.path.basename($shared_in.__str__)) + ":'" + $shared_out.__str__] | |
| 29 #end if | 36 #end if |
| 30 #if $taxonomy_in.__str__ != "None" and len($taxonomy_in.__str__) > 0: | 37 #if $taxonomy_in.__str__ != "None" and len($taxonomy_in.__str__) > 0: |
| 31 --taxonomy=$taxonomy_in | 38 --taxonomy=$taxonomy_in |
| 32 #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__)) + ":'" + $taxonomy_out.__str__] |
| 33 #end if | 40 #end if |
| 34 --result=#echo ','.join($results) | 41 --result=#echo ','.join($results) |
| 35 </command> | 42 </command> |
| 36 <inputs> | 43 <inputs> |
| 37 <param name="group_in" type="data" format="groups" label="group - Groups"/> | 44 <param name="group_in" type="data" format="groups" label="group - Groups"/> |
| 38 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true"> | 45 <conditional name="groupnames"> |
| 39 <options from_dataset="group_in"> | 46 <param name="source" type="select" label="Select Group Names from"> |
| 40 <column name="name" index="1"/> | 47 <option value="groups">A List of Group Names</option> |
| 41 <column name="value" index="1"/> | 48 <option value="accnos">A History Group Name Accnos Dataset</option> |
| 42 <filter type="unique_value" name="unq_grp" column="1" /> | 49 </param> |
| 43 </options> | 50 <when value="groups"> |
| 44 </param> | 51 <param name="groups" type="select" label="groups - Pick groups to include" multiple="true"> |
| 45 <param name="accnos" type="data" format="accnos" optional="true" label="accnos - Accession Names"/> | 52 <options from_dataset="group_in"> |
| 46 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/> | 53 <column name="name" index="1"/> |
| 54 <column name="value" index="1"/> | |
| 55 <filter type="unique_value" name="unq_grp" column="1" /> | |
| 56 </options> | |
| 57 </param> | |
| 58 </when> | |
| 59 <when value="accnos"> | |
| 60 <param name="accnos" type="data" format="accnos" label="accnos - Group Names from your history"/> | |
| 61 </when> | |
| 62 </conditional> | |
| 63 <param name="fasta_in" type="data" format="fasta,align" optional="true" label="fasta - Fasta Sequences"/> | |
| 47 <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/> | 64 <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/> |
| 48 <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/> | 65 <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"/> | |
| 49 <param name="taxonomy_in" type="data" format="seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> | 67 <param name="taxonomy_in" type="data" format="seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> |
| 50 </inputs> | 68 </inputs> |
| 51 <outputs> | 69 <outputs> |
| 52 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | 70 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
| 53 <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"/> | 71 <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"/> |
| 58 <data format="names" name="name_out" label="${tool.name} on ${on_string}: pick.name"> | 76 <data format="names" name="name_out" label="${tool.name} on ${on_string}: pick.name"> |
| 59 <filter>name_in != None</filter> | 77 <filter>name_in != None</filter> |
| 60 </data> | 78 </data> |
| 61 <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"> | 79 <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"> |
| 62 <filter>list_in != None</filter> | 80 <filter>list_in != None</filter> |
| 81 </data> | |
| 82 <data format="shared" name="shared_out" label="${tool.name} on ${on_string}: pick.shared"> | |
| 83 <filter>shared_in != None</filter> | |
| 63 </data> | 84 </data> |
| 64 <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"> | 85 <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"> |
| 65 <filter>taxonomy_in != None</filter> | 86 <filter>taxonomy_in != None</filter> |
| 66 </data> | 87 </data> |
| 67 </outputs> | 88 </outputs> |
| 79 | 100 |
| 80 .. _Mothur: http://www.mothur.org/wiki/Main_Page | 101 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
| 81 | 102 |
| 82 **Command Documenation** | 103 **Command Documenation** |
| 83 | 104 |
| 84 The get.groups_ command selects sequences from a specific group or set of groups from the following file types: fasta, name, group, list, taxonomy. | 105 The get.groups_ command selects sequences from a specific group or set of groups from the following file types: fasta, fasta, name_, group_, list_, taxonomy_. |
| 85 | 106 |
| 107 .. _name: http://www.mothur.org/wiki/Name_file | |
| 108 .. _group: http://www.mothur.org/wiki/Group_file | |
| 109 .. _list: http://www.mothur.org/wiki/List_file | |
| 110 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline | |
| 86 .. _get.groups: http://www.mothur.org/wiki/Get.groups | 111 .. _get.groups: http://www.mothur.org/wiki/Get.groups |
| 87 | 112 |
| 88 | 113 |
| 89 </help> | 114 </help> |
| 90 </tool> | 115 </tool> |