Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/merge.groups.xml @ 33:d53b9eb16c2d
mothur_wrapper.py - convert_value needs to return a String
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Wed, 11 Sep 2013 16:56:31 -0500 |
parents | 49058b1f8d3f |
children | 95d75b35e4d2 |
rev | line source |
---|---|
24
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1 <tool id="mothur_merge_groups" name="Merge.groups" version="1.24.0" > |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
2 <description>Merge groups in a shared file</description> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
3 <command interpreter="python"> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
4 mothur_wrapper.py |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
5 --cmd='merge.groups' |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
6 ## 98_sq_phylip_amazon.fn.merge.shared |
24
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
7 #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
8 --outputdir='$logfile.extra_files_path' |
24
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
9 #if $otu.__str__ != "None" and len($otu.__str__) > 0: |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
10 --shared=$otu |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
11 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.merge.\2',$os.path.basename($otu.__str__)) + ":'" + $merge_shared.__str__] |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
12 #end if |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
13 #if $group.__str__ != "None" and len($group.__str__) > 0: |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
14 --group=$group |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
15 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.merge.\2',$os.path.basename($group.__str__)) + ":'" + $merge_group.__str__] |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
16 #end if |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
17 #if $design.source == 'hist': |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
18 --design=$design_dataset |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
19 #else: |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
20 --design=$generated_design |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
21 #end if |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
22 #if $groups.__str__ != "None" and len($groups.__str__) > 0: |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
23 --groups=$groups |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
24 #end if |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
25 #if $label.__str__ != "None" and len($label.__str__) > 0: |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
26 --label='$label' |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
27 #end if |
24
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
28 --result=#echo ','.join($results) |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
29 </command> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
30 <inputs> |
24
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
31 <param name="otu" type="data" format="shared" optional="true" label="shared - OTU Shared Dataset"/> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
32 <param name="group" type="data" format="groups" optional="true" label="group - Group Dataset"/> |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
33 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" 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:
24
diff
changeset
|
34 <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:
24
diff
changeset
|
35 <filter type="data_meta" ref="otu" key="groups" /> |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
36 </options> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
37 </param> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
38 <param name="label" type="select" label="label - Pick OTU Labels to include" optional="true" 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:
24
diff
changeset
|
39 <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:
24
diff
changeset
|
40 <filter type="data_meta" ref="otu" key="labels" /> |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
41 </options> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
42 </param> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
43 <conditional name="design"> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
44 <param name="source" type="select" label="Grouping Design from" help=""> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
45 <option value="hist">Your History</option> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
46 <option value="build">Build a grouping design</option> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
47 </param> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
48 <when value="hist"> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
49 <param name="design_dataset" type="data" format="tabular" label="design - assign groups to new grouping" |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
50 help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
51 </when> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
52 <when value="build"> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
53 <repeat name="groupings" title="Grouping"> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
54 <param name="name" type="text" label="Name for a new combined grouping"/> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
55 <param name="groups" type="select" multiple="true" label="Select groups for to include in this grouping"> |
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:
24
diff
changeset
|
56 <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:
24
diff
changeset
|
57 <filter type="data_meta" ref="otu" key="groups" /> |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
58 </options> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
59 </param> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
60 </repeat> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
61 </when> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
62 </conditional> <!-- design --> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
63 </inputs> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
64 <configfiles> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
65 <configfile name="generated_design"> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
66 #if $design.source == 'build': |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
67 #for $grouping in $design.groupings: |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
68 #set grp_str = $grouping.groups.__str__ |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
69 #if grp_str != None and len(grp_str) > 0: |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
70 #for $grp in grp_str.split(','): |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
71 $grp $grouping.name |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
72 #end for |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
73 #end if |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
74 #end for |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
75 #end if |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
76 </configfile> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
77 </configfiles> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
78 <outputs> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
79 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
24
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
80 <data format="shared" name="merged_shared" label="${tool.name} on ${on_string}: merge.shared" > |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
81 <filter>otu != None</filter> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
82 </data> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
83 <data format="groups" name="merged_group" label="${tool.name} on ${on_string}: merge.groups" > |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
84 <filter>groups != None</filter> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
85 </data> |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
86 </outputs> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
87 <requirements> |
27
49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
Jim Johnson <jj@umn.edu>
parents:
25
diff
changeset
|
88 <requirement type="package" version="1.27">mothur</requirement> |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
89 </requirements> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
90 <tests> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
91 </tests> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
92 <help> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
93 **Mothur Overview** |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
94 |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
95 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
96 in the Department of Microbiology and Immunology at The University of Michigan, |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
97 provides bioinformatics for the microbial ecology community. |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
98 |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
99 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
100 |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
101 **Command Documenation** |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
102 |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
103 The merge.groups_ command reads a shared_ file and a design file and merges the groups in the shared file that are in the same grouping in the design file. |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
104 |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
105 A design file partitions a list of names into groups. It is a tab-delimited file with 2 columns: name and group, e.g. : |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
106 ======= ======= |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
107 duck bird |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
108 cow mammal |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
109 pig mammal |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
110 goose bird |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
111 cobra reptile |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
112 ======= ======= |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
113 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
114 The Make_Design tool can construct a design file from a Mothur dataset that contains group names. |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
115 |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
116 .. _shared: http://www.mothur.org/wiki/Shared_file |
1
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
117 .. _merge.groups: http://www.mothur.org/wiki/Merge.groups |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
118 |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
119 </help> |
fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
120 </tool> |