Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/pca.xml @ 2:e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:39:06 -0400 |
parents | fcc0778f6987 |
children | 7bfe1f843858 |
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1:fcc0778f6987 | 2:e990ac8a0f58 |
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1 <tool id="mothur_pca" name="Pca" version="1.16.0"> | 1 <tool id="mothur_pca" name="Pca" version="1.19.0"> |
2 <description>generate principle components plot data</description> | 2 <description>Principal Coordinate Analysis for a shared file</description> |
3 <command interpreter="python"> | 3 <command interpreter="python"> |
4 mothur_wrapper.py | 4 mothur_wrapper.py |
5 ## 98_sq_phylip_amazon.fn.unique.pca.axes | 5 ## 98_sq_phylip_amazon.fn.unique.pca.axes |
6 ## 98_sq_phylip_amazon.fn.unique.pca.loadings | 6 ## 98_sq_phylip_amazon.fn.unique.pca.loadings |
7 --cmd='pca' | 7 --cmd='pca' |
8 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.pca.axes$:'$pca_axes,'^\S+\.pca.loadings$:'$pca_loadings | 8 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.pca.axes$:'$pca_axes,'^\S+\.pca.loadings$:'$pca_loadings |
9 --outputdir='$logfile.extra_files_path' | 9 --outputdir='$logfile.extra_files_path' |
10 --READ_cmd='read.otu' | 10 #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): |
11 #if $input.source == 'similarity': | 11 --shared=$otu |
12 --READ_list=$input.otu | 12 #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('relabund').__class__): |
13 #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0: | 13 --relabund=$otu |
14 --READ_group='$otu_group' | 14 #end if |
15 #end if | 15 #if $label.__str__ != "None" and len($label.__str__) > 0: |
16 #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: | 16 --label='$label' |
17 --READ_groups='$input.groups' | 17 #end if |
18 #end if | 18 #if $groups.__str__ != "None" and len($groups.__str__) > 0: |
19 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: | 19 --groups='$groups' |
20 --READ_label='$input.label' | |
21 #end if | |
22 #elif $input.source == 'shared': | |
23 --READ_shared=$input.otu | |
24 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: | |
25 --READ_label='$input.label' | |
26 #end if | |
27 #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: | |
28 --READ_groups='$input.groups' | |
29 #end if | |
30 #end if | 20 #end if |
31 $metric | 21 $metric |
32 </command> | 22 </command> |
33 <inputs> | 23 <inputs> |
34 <conditional name="input"> | 24 <param name="otu" type="data" format="shared,relabund" label="shared,relabund - OTU Shared or Relabund file"/> |
35 <param name="source" type="select" label="Generate principle components for"> | 25 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
36 <option value="similarity">OTU list</option> | 26 <options from_dataset="otu"> |
37 <option value="shared">OTU Shared</option> | 27 <column name="name" index="0"/> |
38 </param> | 28 <column name="value" index="0"/> |
39 <when value="similarity"> | 29 <filter type="unique_value" name="unq_lbl" column="0" /> |
40 <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/> | 30 </options> |
41 <param name="otu_group" type="data" format="groups" label="read.otu(group=) - Group file for the OTU List"/> | 31 </param> |
42 <param name="label" type="select" label="label - OTU Labels" multiple="true"> | 32 <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> |
43 <options from_dataset="otu"> | 33 <options from_dataset="otu"> |
44 <column name="name" index="0"/> | 34 <column name="name" index="1"/> |
45 <column name="value" index="0"/> | 35 <column name="value" index="1"/> |
46 </options> | 36 <filter type="unique_value" name="unq_grp" column="1" /> |
47 </param> | 37 </options> |
48 <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> | 38 </param> |
49 <options from_dataset="otu_group"> | 39 <param name="metric" type="boolean" truevalue="" falsevalue="--metric=False" checked="true" label="metric - Calculate pearson correlation coefficient" /> |
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> | |
56 <when value="shared"> | |
57 <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/> | |
58 <param name="label" type="select" label="label - OTU Labels" multiple="true"> | |
59 <options from_dataset="otu"> | |
60 <column name="name" index="0"/> | |
61 <column name="value" index="0"/> | |
62 <filter type="unique_value" name="unq_lbl" column="0" /> | |
63 </options> | |
64 </param> | |
65 <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> | |
66 <options from_dataset="otu"> | |
67 <column name="name" index="1"/> | |
68 <column name="value" index="1"/> | |
69 <filter type="unique_value" name="unq_grp" column="1" /> | |
70 </options> | |
71 </param> | |
72 </when> | |
73 </conditional> | |
74 <param name="metric" type="boolean" truevalue="" falsevalue="--Metric=False" checked="true" label="metric - Calculate pearson correlation coefficient" /> | |
75 </inputs> | 40 </inputs> |
76 <outputs> | 41 <outputs> |
77 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | 42 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
78 <data format="axes" name="pca_axes" label="${tool.name} on ${on_string}: pca.axes" /> | 43 <data format="axes" name="pca_axes" label="${tool.name} on ${on_string}: pca.axes" /> |
79 <data format="txt" name="pca_loadings" label="${tool.name} on ${on_string}: pca.loadings" /> | 44 <data format="txt" name="pca_loadings" label="${tool.name} on ${on_string}: pca.loadings" /> |
92 | 57 |
93 .. _Mothur: http://www.mothur.org/wiki/Main_Page | 58 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
94 | 59 |
95 **Command Documenation** | 60 **Command Documenation** |
96 | 61 |
97 The pca_ command generate principle components plot data. | 62 The pca_ command generate principle components plot data for a shared_ or relabund_ file. |
98 | 63 |
64 .. _shared: http://www.mothur.org/wiki/Shared_file | |
65 .. _relabund: http://www.mothur.org/wiki/Get.relabund | |
99 .. _pca: http://www.mothur.org/wiki/Pca | 66 .. _pca: http://www.mothur.org/wiki/Pca |
100 | 67 |
101 </help> | 68 </help> |
102 </tool> | 69 </tool> |