Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/get.sharedseqs.xml @ 36:040410b8167e default tip
Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information.
author | galaxyuser <galaxy_user@agr.g.ca> |
---|---|
date | Mon, 10 Nov 2014 15:40:02 -0500 |
parents | 95d75b35e4d2 |
children |
rev | line source |
---|---|
35
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
1 <tool id="mothur_get_sharedseqs" name="Get.sharedseqs" version="1.21.0" force_history_refresh="True"> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
2 <description>Get shared sequences at each distance from list and group</description> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
3 <command interpreter="python"> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
4 mothur_wrapper.py |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
5 #import re, os.path |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
6 --cmd='get.sharedseqs' |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
7 --result='^mothur.\S+\.logfile$:'$logfile |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
8 --outputdir='$logfile.extra_files_path' |
35
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
9 #if isinstance($list.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__): |
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
10 --list=$list |
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
11 --group=$group |
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
12 #else |
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
13 --shared=$list |
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
14 #end if |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
15 #set datasets = ["'^\S+?\.((unique|[0-9.]*)(\S+)\.shared.seqs)$:tabular'"] |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
16 #if $label.__str__ != "None" and len($label.__str__) > 0: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
17 --label='$label' |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
18 #end if |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
19 #if $seqs_from.selection == 'unique': |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
20 #if $seqs_from.groups.__str__ != "None" and len($seqs_from.groups.__str__) > 0: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
21 --unique=$seqs_from.groups |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
22 #end if |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
23 #elif $seqs_from.selection == 'shared': |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
24 #if $seqs_from.groups.__str__ != "None" and len($seqs_from.groups.__str__) > 0: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
25 --shared=$seqs_from.groups |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
26 #end if |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
27 #end if |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
28 #if $fasta.__str__ != "None" and len($fasta.__str__) > 0: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
29 --fasta=$fasta |
4 | 30 #set datasets = $datasets + ["'^\S+?\.((unique|[0-9.]*)(\S+)\.shared.fasta)$:" + $fasta.ext + "'"] |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
31 #end if |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
32 #if $output.__str__ != "None" and len($output.__str__) > 0: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
33 --output=$output |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
34 #set datasets = $datasets + ["'^\S+?\.((unique|[0-9.]*)(\S+)\.accnos)$:accnos'"] |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
35 #end if |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
36 #if $as_datasets.__str__ == "yes": |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
37 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
38 --new_datasets=#echo ','.join($datasets) |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
39 #end if |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
40 </command> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
41 <inputs> |
35
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
42 <param name="list" type="data" format="list,shared" label="list - OTU List or shared file"/> |
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
43 <param name="group" type="data" format="groups" label="group - not required if using a shared file"/> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
44 <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
45 help="By default all are included if no selection is made."> |
25
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
12
diff
changeset
|
46 <options> |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
12
diff
changeset
|
47 <filter type="data_meta" ref="list" key="labels" /> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
48 </options> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
49 </param> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
50 <param name="fasta" type="data" format="fasta" optional="true" label="fasta - Dataset"/> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
51 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
52 <conditional name="seqs_from"> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
53 <param name="selection" type="select" label="Select Groups" help=""> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
54 <option value="all" selected="true">None (use all groups)</option> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
55 <option value="unique">OTUs that contain ONLY sequences from the selected groups</option> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
56 <option value="shared">OTUs that contain sequences from the selected groups</option> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
57 </param> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
58 <when value="all"/> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
59 <when value="unique"> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
60 <param name="groups" type="select" label="unique - Group to analyze" multiple="true"> |
25
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
12
diff
changeset
|
61 <options> |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
12
diff
changeset
|
62 <filter type="data_meta" ref="group" key="groups" /> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
63 </options> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
64 </param> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
65 </when> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
66 <when value="shared"> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
67 <param name="groups" type="select" label="shared - Groups to analyze" multiple="true"> |
25
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
12
diff
changeset
|
68 <options> |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
Jim Johnson <jj@umn.edu>
parents:
12
diff
changeset
|
69 <filter type="data_meta" ref="group" key="groups" /> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
70 </options> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
71 </param> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
72 </when> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
73 </conditional> <!-- seqs_from --> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
74 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
75 <param name="output" type="select" label="output - select the output format" help="accnos can be used with get.seqs, list.seqs and remove.seqs"> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
76 <option value="" selected="true">default: (name group bin_number)</option> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
77 <option value="accnos">accnos (name)</option> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
78 </param> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
79 <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each label"/> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
80 </inputs> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
81 <outputs> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
82 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
83 </outputs> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
84 <requirements> |
35
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
85 <requirement type="package" version="1.33">mothur</requirement> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
86 </requirements> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
87 <tests> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
88 </tests> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
89 <help> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
90 **Mothur Overview** |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
91 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
92 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
93 in the Department of Microbiology and Immunology at The University of Michigan, |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
94 provides bioinformatics for the microbial ecology community. |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
95 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
96 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
97 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
98 **Command Documenation** |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
99 |
12
370b3fc4e7d3
Mothur galaxy tool updates for Mothur version 1.21.0, fix help section warnings
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
100 The get.sharedseqs_ command takes a list and group file and outputs a .shared.seqs file for each distance. This is useful for those cases where you might be interested in identifying sequences that are either unique or shared by specific groups, which you could then classify. |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
101 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
102 .. _get.sharedseqs: http://www.mothur.org/wiki/Get.sharedseqs |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
103 |
35
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
104 v1.21.0: Updated to Mothur 1.33, added shared file option |
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
105 |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
106 </help> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
107 </tool> |