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comparison mothur/tools/mothur/tree.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_tree_shared" name="Tree.shared" version="1.16.0" force_history_refresh="True"> 1 <tool id="mothur_tree_shared" name="Tree.shared" version="1.19.0" force_history_refresh="True">
2 <description>Generate a newick tree for dissimilarity among groups</description> 2 <description>Generate a newick tree for dissimilarity among groups</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 mothur_wrapper.py 4 mothur_wrapper.py
5 --cmd='tree.shared' 5 --cmd='tree.shared'
6 --result='^mothur.\S+\.logfile$:'$logfile 6 #if $input.source == 'shared':
7 --outputdir='$logfile.extra_files_path' 7 --result='^mothur.\S+\.logfile$:'$logfile
8 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' 8 #if $input.as_datasets.__str__ == "yes":
9 --new_datasets='^\S+?([a-z]+\.(unique|[0-9.]*)\.tre)$:tre' 9 --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
10 --READ_cmd='read.otu' 10 --new_datasets='^\S+?([a-z]+\.(unique|[0-9.]*)\.tre)$:tre'
11 #if $input.source == 'similarity': 11 #end if
12 --READ_list=$input.otu 12 --shared=$input.dist
13 #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0: 13 #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
14 --READ_group='$otu_group' 14 --groups=$input.groups
15 #end if 15 #end if
16 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: 16 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
17 --READ_label='$input.label' 17 --label='$input.label'
18 #end if 18 #end if
19 #elif $input.source == 'shared': 19 #else:
20 --READ_shared=$input.otu 20 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.tre$:'$tre
21 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: 21 --outputdir='$logfile.extra_files_path'
22 --READ_label='$input.label' 22 #if $input.source == 'column':
23 --column=$input.dist
24 --name=$input.name
25 #elif $input.source == 'phylip':
26 --phylip=$input.dist
27 #if $input.name.__str__ != "None" and len($input.name.__str__) > 0:
28 --name=$input.name
29 #end if
23 #end if 30 #end if
24 #end if
25 #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
26 --groups=$input.groups
27 #end if 31 #end if
28 #if $calc.__str__ != "None" and len($calc.__str__) > 0: 32 #if $calc.__str__ != "None" and len($calc.__str__) > 0:
29 --calc=$calc 33 --calc=$calc
30 #end if 34 #end if
31 </command> 35 </command>
32 <inputs> 36 <inputs>
33 <!-- list,group or shared --> 37 <!-- column,name phylip or shared -->
34 <conditional name="input"> 38 <conditional name="input">
35 <param name="source" type="select" label="Generate Heatmap for"> 39 <param name="source" type="select" label="Select input format">
36 <option value="similarity">OTU list</option>
37 <option value="shared">OTU Shared</option> 40 <option value="shared">OTU Shared</option>
41 <option value="column">Pairwise Column Distance Matrix</option>
42 <option value="phylip">Phylip Distance Matrix</option>
38 </param> 43 </param>
39 <when value="similarity"> 44 <when value="column">
40 <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/> 45 <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/>
41 <param name="otu_group" type="data" format="groups" label="read.otu(group=) - Group file for the OTU List"/> 46 <param name="name" type="data" format="names" label="name - Sequences Name reference"/>
42 <param name="label" type="select" label="label - OTU Labels" multiple="true"> 47 </when>
43 <options from_dataset="otu"> 48 <when value="phylip">
44 <column name="name" index="0"/> 49 <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/>
45 <column name="value" index="0"/> 50 <param name="name" type="data" format="names" optional="true" label="name - Names"/>
46 </options>
47 </param>
48 <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
49 <options from_dataset="otu_group">
50 <column name="name" index="1"/>
51 <column name="value" index="1"/>
52 <filter type="unique_value" name="unq_grp" column="1" />
53 </options>
54 </param>
55 </when> 51 </when>
56 <when value="shared"> 52 <when value="shared">
57 <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/> 53 <param name="dist" type="data" format="shared" label="shared - OTU Shared"/>
54 <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each label and calculator"/>
58 <param name="label" type="select" label="label - OTU Labels" multiple="true"> 55 <param name="label" type="select" label="label - OTU Labels" multiple="true">
59 <options from_dataset="otu"> 56 <options from_dataset="dist">
60 <column name="name" index="0"/> 57 <column name="name" index="0"/>
61 <column name="value" index="0"/> 58 <column name="value" index="0"/>
62 <filter type="unique_value" name="unq_lbl" column="0" /> 59 <filter type="unique_value" name="unq_lbl" column="0" />
63 </options> 60 </options>
64 </param> 61 </param>
65 <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> 62 <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
66 <options from_dataset="otu"> 63 <options from_dataset="dist">
67 <column name="name" index="1"/> 64 <column name="name" index="1"/>
68 <column name="value" index="1"/> 65 <column name="value" index="1"/>
69 <filter type="unique_value" name="unq_grp" column="1" /> 66 <filter type="unique_value" name="unq_grp" column="1" />
70 </options> 67 </options>
71 </param> 68 </param>
80 </options> 77 </options>
81 </param> 78 </param>
82 </inputs> 79 </inputs>
83 <outputs> 80 <outputs>
84 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> 81 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
82 <data format="tre" name="tre" label="${tool.name} on ${on_string}: tre">
83 <filter>input['source'] != 'shared'</filter>
84 </data>
85 </outputs> 85 </outputs>
86 <requirements> 86 <requirements>
87 <requirement type="binary">mothur</requirement> 87 <requirement type="binary">mothur</requirement>
88 </requirements> 88 </requirements>
89 <tests> 89 <tests>
97 97
98 .. _Mothur: http://www.mothur.org/wiki/Main_Page 98 .. _Mothur: http://www.mothur.org/wiki/Main_Page
99 99
100 **Command Documenation** 100 **Command Documenation**
101 101
102 The tree.shared_ command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups. 102 The tree.shared_ command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups. For calc parameter choices see: http://www.mothur.org/wiki/Calculators
103 103
104 .. _tree.shared: http://www.mothur.org/wiki/Tree.shared 104 .. _tree.shared: http://www.mothur.org/wiki/Tree.shared
105 105
106 106
107 </help> 107 </help>