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comparison mothur/tools/mothur/summary.shared.xml @ 2:e990ac8a0f58

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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author jjohnson
date Tue, 07 Jun 2011 17:39:06 -0400
parents fcc0778f6987
children 7bfe1f843858
comparison
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1:fcc0778f6987 2:e990ac8a0f58
1 <tool id="mothur_summary_shared" name="Summary.shared" version="1.16.0" force_history_refresh="True"> 1 <tool id="mothur_summary_shared" name="Summary.shared" version="1.19.0" force_history_refresh="True">
2 <description>Summary of calculator values for OTUs</description> 2 <description>Summary of calculator values for OTUs</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 mothur_wrapper.py 4 mothur_wrapper.py
5 --cmd='summary.shared' 5 --cmd='summary.shared'
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.summary$:'$summary 6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.summary$:'$summary
7 --outputdir='$logfile.extra_files_path' 7 --outputdir='$logfile.extra_files_path'
8 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' 8 --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
9 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist' 9 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist'
10 --READ_cmd='read.otu' 10 --shared=$otu
11 #if $input.source == 'similarity': 11 #if $groups.__str__ != "None" and len($groups.__str__) > 0:
12 --READ_list=$input.otu 12 --groups=$groups
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 13 #end if
33 #if $label.__str__ != "None" and len($label.__str__) > 0: 14 #if $label.__str__ != "None" and len($label.__str__) > 0:
34 --label='$label' 15 --label='$label'
35 #end if 16 #end if
36 *#
37 #if $calc.__str__ != "None" and len($calc.__str__) > 0: 17 #if $calc.__str__ != "None" and len($calc.__str__) > 0:
38 --calc='$calc' 18 --calc='$calc'
39 #end if 19 #end if
40 $all 20 $all
21 $distance
41 </command> 22 </command>
42 <inputs> 23 <inputs>
43 <!-- list,group or shared --> 24 <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/>
44 <conditional name="input"> 25 <param name="label" type="select" label="label - OTU Labels" multiple="true">
45 <param name="source" type="select" label="Generate Collector Curvers for"> 26 <options from_dataset="otu">
46 <option value="similarity">OTU list</option> 27 <column name="name" index="0"/>
47 <option value="shared">OTU Shared</option> 28 <column name="value" index="0"/>
48 </param> 29 <filter type="unique_value" name="unq_lbl" column="0" />
49 <when value="similarity"> 30 </options>
50 <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/> 31 </param>
51 <param name="otu_group" type="data" format="groups" label="read.otu(group=) - Group file for the OTU List"/> 32 <param name="groups" type="select" label="groups - Pairwise comparision groups" multiple="true">
52 <param name="label" type="select" label="label - OTU Labels" multiple="true"> 33 <options from_dataset="otu">
53 <options from_dataset="otu"> 34 <column name="name" index="1"/>
54 <column name="name" index="0"/> 35 <column name="value" index="1"/>
55 <column name="value" index="0"/> 36 <filter type="unique_value" name="unq_grp" column="1" />
56 <filter type="unique_value" name="unq_lbl" column="0" /> 37 </options>
57 </options> 38 </param>
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"> 39 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
86 <options from_file="mothur_calculators.loc"> 40 <options from_file="mothur_calculators.loc">
87 <column name="mult" index="1"/> 41 <column name="mult" index="1"/>
88 <column name="name" index="0"/> 42 <column name="name" index="0"/>
89 <column name="value" index="0"/> 43 <column name="value" index="0"/>
111 65
112 .. _Mothur: http://www.mothur.org/wiki/Main_Page 66 .. _Mothur: http://www.mothur.org/wiki/Main_Page
113 67
114 **Command Documenation** 68 **Command Documenation**
115 69
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. 70 The summary.shared_ command produce a summary file that has the calculator value for each line in the OTU data of the shared_ file and for all possible comparisons between the different groups in the group_ file. This can be useful if you aren't interested in generating collector's or rarefaction curves for your multi-sample data analysis. It would be worth your while, however, to look at the collector's curves for the calculators you are interested in to determine how sensitive the values are to sampling. If the values are not sensitive to sampling, then you can trust the values. Otherwise, you need to keep sampling. For calc parameter choices see: http://www.mothur.org/wiki/Calculators
117 71
72 .. _shared: http://www.mothur.org/wiki/Shared_file
73 .. _group: http://www.mothur.org/wiki/Group_file
118 .. _summary.shared: http://www.mothur.org/wiki/Summary.shared 74 .. _summary.shared: http://www.mothur.org/wiki/Summary.shared
119 75
120 </help> 76 </help>
121 </tool> 77 </tool>