Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/heatmap.bin.xml @ 0:3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
author | jjohnson |
---|---|
date | Tue, 07 Jun 2011 17:32:23 -0400 |
parents | |
children | fcc0778f6987 |
rev | line source |
---|---|
0
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
1 <tool id="mothur_heatmap_bin" name="Heatmap.bin" version="1.15.0" force_history_refresh="True"> |
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 OTUs</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.bin' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
6 --result='^mothur.\S+\.logfile$:'$logfile |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
7 --outputdir='$logfile.extra_files_path' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
8 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
9 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.heatmap\.bin\.svg)$:svg' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
10 --READ_cmd='read.otu' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
11 #if $input.source == 'similarity': |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
12 --READ_list=$input.otu |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
13 #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
14 --READ_group='$otu_group' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
15 #end if |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
16 #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
|
17 --READ_label='$input.label' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
18 #end if |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
19 #elif $input.source == 'shared': |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
20 --READ_relabund=$input.otu |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
21 #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
|
22 --READ_label='$input.label' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
23 #end if |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
24 #end if |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
25 #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
|
26 --groups=$input.groups |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
27 #end if |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
28 #if $scale.__str__ != "None" and len($scale.__str__) > 0: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
29 --scale='$scale' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
30 #end if |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
31 #if $sorted.__str__ != "None" and len($sorted.__str__) > 0: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
32 --sorted='$sorted' |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
33 #end if |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
34 #if $numotu > 0: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
35 --numotu=$numotu |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
36 #end if |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
37 #if 100 > $fontsize > 0: |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
38 --fontsize=$fontsize |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
39 #end if |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
40 </command> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
41 <inputs> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
42 <!-- get.relabund relabund type should also work --> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
43 <conditional name="input"> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
44 <param name="source" type="select" label="Generate Heatmap for"> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
45 <option value="similarity">OTU list</option> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
46 <option value="relabund">OTU Relative Abundance</option> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
47 </param> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
48 <when value="similarity"> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
49 <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
50 <param name="otu_group" type="data" format="groups" label="read.otu(group) - Group file for the OTU List"/> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
51 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
52 <options from_dataset="otu"> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
53 <column name="name" index="0"/> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
54 <column name="value" index="0"/> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
55 </options> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
56 </param> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
57 <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
58 <options from_dataset="otu_group"> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
59 <column name="name" index="1"/> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
60 <column name="value" index="1"/> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
61 <filter type="unique_value" name="unq_grp" column="1" /> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
62 </options> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
63 </param> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
64 </when> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
65 <when value="relabund"> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
66 <param name="otu" type="data" format="relabund" label="read.otu(relabund=) - OTU Relative Abundance"/> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
67 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
68 <options from_dataset="otu"> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
69 <column name="name" index="0"/> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
70 <column name="value" index="0"/> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
71 </options> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
72 </param> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
73 <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
74 <options from_dataset="otu"> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
75 <column name="name" index="1"/> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
76 <column name="value" index="1"/> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
77 <filter type="unique_value" name="unq_grp" column="1" /> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
78 </options> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
79 </param> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
80 </when> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
81 </conditional> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
82 <param name="scale" type="select" label="scale - Scaling for heatmap"> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
83 <option value="">Default</option> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
84 <option value="log10">Log10</option> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
85 <option value="log2">Log2</option> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
86 <option value="linear">Linear</option> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
87 </param> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
88 <param name="sorted" type="select" label="sorted - Sort heatmap"> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
89 <option value="">By shared</option> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
90 <option value="none">Don't sort</option> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
91 <option value="totalotu">By Total OTUs</option> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
92 <option value="totalgroup">By Total Groups</option> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
93 </param> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
94 <param name="numotu" type="integer" value="0" label="numotu - Limit the number of OTUs displayed (ignored if 0)"/> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
95 <param name="fontsize" type="integer" value="24" label="fontsize - Fontsize (default is 24)"/> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
96 </inputs> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
97 <outputs> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
98 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
99 </outputs> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
100 <requirements> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
101 <requirement type="binary">mothur</requirement> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
102 </requirements> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
103 <tests> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
104 </tests> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
105 <help> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
106 **Mothur Overview** |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
107 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
108 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
|
109 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
|
110 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
|
111 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
112 .. _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
|
113 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
114 **Command Documenation** |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
115 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
116 The heatmap.bin_ command generates a heat map from data provided in either a .list or a .shared file. |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
117 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
118 .. _heatmap.bin: http://www.mothur.org/wiki/Heatmap.bin |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
119 |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
120 </help> |
3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff
changeset
|
121 </tool> |