Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/summary.shared.xml @ 0:3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:32:23 -0400 |
parents | |
children | fcc0778f6987 |
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1 <tool id="mothur_summary_shared" name="Summary.shared" version="1.15.0" force_history_refresh="True"> | |
2 <description>Summary of calculator values for OTUs</description> | |
3 <command interpreter="python"> | |
4 mothur_wrapper.py | |
5 --cmd='summary.shared' | |
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.summary$:'$summary | |
7 --outputdir='$logfile.extra_files_path' | |
8 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' | |
9 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist' | |
10 --READ_cmd='read.otu' | |
11 #if $input.source == 'similarity': | |
12 --READ_list=$input.otu | |
13 #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0: | |
14 --READ_group='$otu_group' | |
15 #end if | |
16 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: | |
17 --READ_label='$input.label' | |
18 #end if | |
19 #elif $input.source == 'shared': | |
20 --READ_shared=$input.otu | |
21 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: | |
22 --READ_label='$input.label' | |
23 #end if | |
24 #end if | |
25 #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: | |
26 --groups=$input.groups | |
27 #end if | |
28 #* | |
29 --READ_list=$otu | |
30 #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0: | |
31 --READ_group='$otu_group' | |
32 #end if | |
33 #if $label.__str__ != "None" and len($label.__str__) > 0: | |
34 --label='$label' | |
35 #end if | |
36 *# | |
37 #if $calc.__str__ != "None" and len($calc.__str__) > 0: | |
38 --calc='$calc' | |
39 #end if | |
40 $all | |
41 </command> | |
42 <inputs> | |
43 <!-- list,group or shared --> | |
44 <conditional name="input"> | |
45 <param name="source" type="select" label="Generate Collector Curvers for"> | |
46 <option value="similarity">OTU list</option> | |
47 <option value="shared">OTU Shared</option> | |
48 </param> | |
49 <when value="similarity"> | |
50 <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/> | |
51 <param name="otu_group" type="data" format="groups" label="read.otu(group=) - Group file for the OTU List"/> | |
52 <param name="label" type="select" label="label - OTU Labels" multiple="true"> | |
53 <options from_dataset="otu"> | |
54 <column name="name" index="0"/> | |
55 <column name="value" index="0"/> | |
56 <filter type="unique_value" name="unq_lbl" column="0" /> | |
57 </options> | |
58 </param> | |
59 <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> | |
60 <options from_dataset="otu_group"> | |
61 <column name="name" index="1"/> | |
62 <column name="value" index="1"/> | |
63 <filter type="unique_value" name="unq_grp" column="1" /> | |
64 </options> | |
65 </param> | |
66 </when> | |
67 <when value="shared"> | |
68 <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/> | |
69 <param name="label" type="select" label="label - OTU Labels" multiple="true"> | |
70 <options from_dataset="otu"> | |
71 <column name="name" index="0"/> | |
72 <column name="value" index="0"/> | |
73 <filter type="unique_value" name="unq_lbl" column="0" /> | |
74 </options> | |
75 </param> | |
76 <param name="groups" type="select" label="groups - Pairwise comparision groups" multiple="true"> | |
77 <options from_dataset="otu"> | |
78 <column name="name" index="1"/> | |
79 <column name="value" index="1"/> | |
80 <filter type="unique_value" name="unq_grp" column="1" /> | |
81 </options> | |
82 </param> | |
83 </when> | |
84 </conditional> | |
85 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> | |
86 <options from_file="mothur_calulators.loc"> | |
87 <column name="mult" index="1"/> | |
88 <column name="name" index="0"/> | |
89 <column name="value" index="0"/> | |
90 <filter type="static_value" name="mult" column="1" value="shared" /> | |
91 </options> | |
92 </param> | |
93 <param name="all" type="boolean" truevalue="--all=true" falsevalue="" checked="false" label="all - Include RAM intensive sharedsobs and sharedchao calculations"/> | |
94 <param name="distance" type="boolean" truevalue="--distance=true" falsevalue="" checked="false" label="distance - Output a distance file for each calculator at each label"/> | |
95 </inputs> | |
96 <outputs> | |
97 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | |
98 <data format="tabular" name="summary" label="${tool.name} on ${on_string}: shared.summary" /> | |
99 </outputs> | |
100 <requirements> | |
101 <requirement type="binary">mothur</requirement> | |
102 </requirements> | |
103 <tests> | |
104 </tests> | |
105 <help> | |
106 **Mothur Overview** | |
107 | |
108 Mothur_, initiated by Dr. Patrick Schloss and his software development team | |
109 in the Department of Microbiology and Immunology at The University of Michigan, | |
110 provides bioinformatics for the microbial ecology community. | |
111 | |
112 .. _Mothur: http://www.mothur.org/wiki/Main_Page | |
113 | |
114 **Command Documenation** | |
115 | |
116 The summary.shared_ command produce a summary file that has the calculator value for each line in the OTU data and for all possible comparisons between the different groups in the group file. | |
117 | |
118 .. _summary.shared: http://www.mothur.org/wiki/Summary.shared | |
119 | |
120 </help> | |
121 </tool> |