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comparison mothur/tools/mothur/collect.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_collect_shared" name="Collect.shared" version="1.16.0" force_history_refresh="True"> 1 <tool id="mothur_collect_shared" name="Collect.shared" version="1.19.0" force_history_refresh="True">
2 <description>Generate collector's curves for calculators on OTUs</description> 2 <description>Generate collector's curves for calculators on OTUs</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 mothur_wrapper.py 4 mothur_wrapper.py
5 --cmd='collect.shared' 5 --cmd='collect.shared'
6 --result='^mothur.\S+\.logfile$:'$logfile 6 --result='^mothur.\S+\.logfile$:'$logfile
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+?\.(anderberg|braycurtis|jabund|jclass|jest|kstest|kulczynski|kulczynskicody|lennon|morisitahorn|ochiai|shared\.ace|shared\.chao|shared\.nseqs|shared\.sobs|sorabund|sorclass|sorest|thetan|thetayc|whittaker)$:tabular' 9 --new_datasets='^\S+?\.(anderberg|braycurtis|jabund|jclass|jest|kstest|kulczynski|kulczynskicody|lennon|morisitahorn|ochiai|shared\.ace|shared\.chao|shared\.nseqs|shared\.sobs|sorabund|sorclass|sorest|thetan|thetayc|whittaker)$:tabular'
10 --READ_cmd='read.otu' 10 --shared=$otu
11 #if $input.source == 'similarity': 11 #if $label.__str__ != "None" and len($label.__str__) > 0:
12 --READ_list=$input.otu 12 --label='$label'
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 13 #end if
25 #if $calc.__str__ != "None" and len($calc.__str__) > 0: 14 #if $calc.__str__ != "None" and len($calc.__str__) > 0:
26 --calc='$calc' 15 --calc='$calc'
27 #end if 16 #end if
28 $all 17 $all
29 #if float($freq.__str__) > 0: 18 #if float($freq.__str__) > 0:
30 --freq=$freq 19 --freq=$freq
31 #end if 20 #end if
32 #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: 21 #if $groups.__str__ != "None" and len($groups.__str__) > 0:
33 --groups=$input.groups 22 --groups=$groups
34 #end if 23 #end if
35 </command> 24 </command>
36 <inputs> 25 <inputs>
37 <conditional name="input"> 26 <param name="otu" type="data" format="shared" label="shared - OTU Shared"/>
38 <param name="source" type="select" label="Generate Collector Curvers for"> 27 <param name="label" type="select" label="label - OTU Label filter" multiple="true">
39 <option value="similarity">OTU list</option> 28 <help>To filter: select labels to include</help>
40 <option value="shared">OTU Shared</option> 29 <options from_dataset="otu">
41 </param> 30 <column name="name" index="0"/>
42 <when value="similarity"> 31 <column name="value" index="0"/>
43 <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/> 32 <filter type="unique_value" name="unq_lbl" column="0" />
44 <param name="otu_group" type="data" format="groups" label="read.otu(group) - Group file for the OTU List"/> 33 </options>
45 <param name="label" type="select" label="label - OTU Labels" multiple="true"> 34 </param>
46 <options from_dataset="otu"> 35 <param name="groups" type="select" label="groups - Groups filter (uses all groups if none are selected)" multiple="true">
47 <column name="name" index="0"/> 36 <help>To filter: select select at least 2 groups</help>
48 <column name="value" index="0"/> 37 <options from_dataset="otu">
49 </options> 38 <column name="name" index="1"/>
50 </param> 39 <column name="value" index="1"/>
51 <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> 40 <filter type="unique_value" name="unq_grp" column="1" />
52 <options from_dataset="otu_group"> 41 </options>
53 <column name="name" index="1"/> 42 </param>
54 <column name="value" index="1"/> 43 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none are selected)" multiple="true">
55 <filter type="unique_value" name="unq_grp" column="1" />
56 </options>
57 </param>
58 </when>
59 <when value="shared">
60 <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/>
61 <param name="label" type="select" label="label - OTU Labels" multiple="true">
62 <options from_dataset="otu">
63 <column name="name" index="0"/>
64 <column name="value" index="0"/>
65 <filter type="unique_value" name="unq_lbl" column="0" />
66 </options>
67 </param>
68 <param name="groups" type="select" label="groups - Groups to condider" multiple="true">
69 <options from_dataset="otu">
70 <column name="name" index="1"/>
71 <column name="value" index="1"/>
72 <filter type="unique_value" name="unq_grp" column="1" />
73 </options>
74 </param>
75 </when>
76 </conditional>
77 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
78 <options from_file="mothur_calculators.loc"> 44 <options from_file="mothur_calculators.loc">
79 <column name="mult" index="1"/> 45 <column name="mult" index="1"/>
80 <column name="name" index="0"/> 46 <column name="name" index="0"/>
81 <column name="value" index="0"/> 47 <column name="value" index="0"/>
82 <filter type="static_value" name="mult" column="1" value="shared" /> 48 <filter type="static_value" name="mult" column="1" value="shared" />
103 69
104 .. _Mothur: http://www.mothur.org/wiki/Main_Page 70 .. _Mothur: http://www.mothur.org/wiki/Main_Page
105 71
106 **Command Documenation** 72 **Command Documenation**
107 73
108 The collect.shared_ command generates collector's curves for calculators, which describe the similarity between communities or their shared richness. Collector's curves describe how richness or diversity change as you sample additional individuals. If a collector's curve becomes parallel to the x-axis, you can be reasonably confident that you have done a good job of sampling and can trust the last value in the curve. 74 The collect.shared_ command generates collector's curves for calculators_, which describe the similarity between communities or their shared richness. Collector's curves describe how richness or diversity change as you sample additional individuals. If a collector's curve becomes parallel to the x-axis, you can be reasonably confident that you have done a good job of sampling and can trust the last value in the curve. For calc parameter choices see: http://www.mothur.org/wiki/Calculators
109 75
76 .. _calculators: http://www.mothur.org/wiki/Calculators
110 .. _collect.shared: http://www.mothur.org/wiki/Collect.shared 77 .. _collect.shared: http://www.mothur.org/wiki/Collect.shared
111 78
112 </help> 79 </help>
113 </tool> 80 </tool>