Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/heatmap.sim.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 |
---|---|
18
697156806162
Mothur - update for Mothur version 1.23.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
1 <tool id="mothur_heatmap_sim" name="Heatmap.sim" version="1.23.0" force_history_refresh="True"> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
2 <description>Generate a heatmap for pariwise similarity</description> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
3 <command interpreter="python"> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
4 mothur_wrapper.py |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
5 --cmd='heatmap.sim' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
6 --outputdir='$logfile.extra_files_path' |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
7 #if $as_datasets.__str__ == "yes": |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
8 #if $input.source == 'shared': |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
9 --result='^mothur.\S+\.logfile$:'$logfile |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
10 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
11 --new_datasets='^\S+?\.((unique|[0-9.]*)(\S+)\.heatmap\.sim\.svg)$:svg' |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
12 #else: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
13 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.heatmap\.sim\.svg$:'$heatmap |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
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:
1
diff
changeset
|
15 #else: |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
16 --result='^mothur.\S+\.logfile$:'$logfile |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
17 #end if |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
18 #if $input.source == 'shared': |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
19 --shared=$input.otu |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
20 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
21 --label='$input.label' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
22 #end if |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
23 #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
24 --groups=$input.groups |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
25 #end if |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
26 #if $input.calc.__str__ != "None" and len($input.calc.__str__) > 0: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
27 --calc='$input.calc' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
28 #end if |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
29 #elif $input.source == 'column': |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
30 --column=$input.dist |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
31 --name=$input.name |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
32 #elif $input.source == 'phylip': |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
33 --phylip=$input.dist |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
34 #end if |
18
697156806162
Mothur - update for Mothur version 1.23.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
35 #if 100 > $fontsize > 0: |
697156806162
Mothur - update for Mothur version 1.23.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
36 --fontsize=$fontsize |
697156806162
Mothur - update for Mothur version 1.23.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
37 #end if |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
38 </command> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
39 <inputs> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
40 <conditional name="input"> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
41 <param name="source" type="select" label="Generate Heatmap for"> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
42 <option value="shared">shared - Sample Similarity - OTU Shared</option> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
43 <option value="phylip">phylip - Phylip Distance Matrix</option> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
44 <option value="column">colomn - Pairwise Column Distance Matrix</option> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
45 </param> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
46 <when value="shared"> |
7 | 47 <param name="otu" type="data" format="shared" label="shared - OTU Shared"/> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
48 <param name="label" type="select" label="label - OTU Labels" 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:
22
diff
changeset
|
49 <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:
22
diff
changeset
|
50 <filter type="data_meta" ref="otu" key="labels" /> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
51 </options> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
52 </param> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
53 <param name="groups" type="select" label="groups - 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:
22
diff
changeset
|
54 <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:
22
diff
changeset
|
55 <filter type="data_meta" ref="otu" key="groups" /> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
56 </options> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
57 </param> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
58 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> |
19
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
18
diff
changeset
|
59 <option value="jclass">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
18
diff
changeset
|
60 <option value="jest" selected="true">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
18
diff
changeset
|
61 <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
18
diff
changeset
|
62 <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
18
diff
changeset
|
63 <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
18
diff
changeset
|
64 <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
18
diff
changeset
|
65 <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
18
diff
changeset
|
66 <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option> |
d86987601022
Move calc options in individual tools and remove tool-data/mothur_calculators.loc
Jim Johnson <jj@umn.edu>
parents:
18
diff
changeset
|
67 <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option> |
22
ed906f8149bb
Mothur - html escape amperand in calculator option label
Jim Johnson <jj@umn.edu>
parents:
19
diff
changeset
|
68 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
69 </param> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
70 </when> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
71 <when value="column"> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
72 <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
73 <param name="name" type="data" format="names" label="name - Names"/> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
74 </when> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
75 <when value="phylip"> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
76 <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
77 </when> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
78 </conditional> |
18
697156806162
Mothur - update for Mothur version 1.23.0
Jim Johnson <jj@umn.edu>
parents:
7
diff
changeset
|
79 <param name="fontsize" type="integer" value="24" label="fontsize - Fontsize (default is 24)"/> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
80 <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each image"/> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
81 </inputs> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
82 <outputs> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
83 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
84 <data format="svg" name="heatmap" label="${tool.name} on ${on_string}: heatmap.sim.svg"> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
85 <filter>as_datasets != 'true' and input['source'] != 'shared'</filter> |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
86 </data> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
87 </outputs> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
88 <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
|
89 <requirement type="package" version="1.27">mothur</requirement> |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
90 </requirements> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
91 <tests> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
92 </tests> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
93 <help> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
94 **Mothur Overview** |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
95 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
96 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
97 in the Department of Microbiology and Immunology at The University of Michigan, |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
98 provides bioinformatics for the microbial ecology community. |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
99 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
100 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
101 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
102 **Command Documenation** |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
103 |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
104 The heatmap.sim_ command generates a heat map from data provided in either a shared_ file, a phylip_ distance matrix, or a column_ distance matrix and a name_ file. For calc parameter choices see: http://www.mothur.org/wiki/Calculators |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
105 |
2
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
106 .. _shared: http://www.mothur.org/wiki/Shared_file |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
107 .. _phylip: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
108 .. _column: http://www.mothur.org/wiki/Column-formatted_distance_matrix |
e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents:
1
diff
changeset
|
109 .. _name: http://www.mothur.org/wiki/Name_file |
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
110 .. _heatmap.sim: http://www.mothur.org/wiki/Heatmap.sim |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
111 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
112 </help> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
113 </tool> |