Mercurial > repos > iuc > mothur_otu_association

comparison otu.association.xml @ 0:4b4ca5a8e3e2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:51:08 -0400
parents
children 3c42f300324e
comparison
equal deleted inserted replaced
-1:000000000000 0:4b4ca5a8e3e2
1 <tool profile="16.07" id="mothur_otu_association" name="Otu.association" version="@WRAPPER_VERSION@.0">
2 <description>Calculate the correlation coefficient for the otus</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$otu" otu.dat &&
14 ln -s "$metadata" metadata.dat &&
15
16 echo 'otu.association(
17 #if $otu.is_of_type("mothur.relabund"):
18 relabund=otu.dat
19 #elif $otu.is_of_type("mothur.shared"):
20 shared=otu.dat
21 #end if
22 #if $label:
23 ,label=${ str($label).replace(",","-") }
24 #end if
25 #if $groups:
26 ,groups=${ str($groups).replace(",","-") }
27 #end if
28 #if $method:
29 ,method=$method
30 #end if
31 #if $metadata:
32 ,metadata=metadata.dat
33 #end if
34 #if $cutoff:
35 ,cutoff=$cutoff
36 #end if
37 )'
38 | sed 's/ //g' ## mothur trips over whitespace
39 | mothur
40 | tee mothur.out.log
41 ]]></command>
42 <inputs>
43 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/>
44 <param name="label" type="select" label="label - OTU Labels" multiple="true" help="By default all labels are used">
45 <expand macro="labeloptions"/>
46 </param>
47 <param name="groups" type="select" label="groups - Groups to include" multiple="true">
48 <options>
49 <filter type="data_meta" ref="otu" key="groups"/>
50 </options>
51 </param>
52 <param name="method" type="select" label="method - Normalization method">
53 <option value="pearson" selected="true">pearson</option>
54 <option value="spearman">spearman</option>
55 <option value="kendall">kendall</option>
56 </param>
57 <param name="metadata" type="data" format="tabular" optional="true" label="metadata - find the association between the otus and the metadata."/>
58 <param name="cutoff" type="float" value="" min="0" max="1" optional="true" label="cutoff - set a pvalue at which the otu will be reported"/>
59 </inputs>
60 <outputs>
61 <expand macro="logfile-output"/>
62 <collection name="correlations" type="list" label="${tool.name} on ${on_string}: correlation coefficient files per OTU label">
63 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.otu\.corr" format="mothur.otu.corr"/>
64 </collection>
65 </outputs>
66 <tests>
67 <test><!-- test with shared file and default settings -->
68 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
69 <output_collection name="correlations" count="36">
70 <element name="0.41.pearson" md5="ba93b529a7b0e5ca3baa8fe9a41b4107" ftype="mothur.otu.corr"/>
71 </output_collection>
72 <expand macro="logfile-test"/>
73 </test>
74 <test><!-- test with relabund file and label and group select -->
75 <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/>
76 <param name="method" value="kendall"/>
77 <param name="label" value="0.03,0.05,0.36,0.41,0.55"/>
78 <param name="groups" value="forest,pasture"/>
79 <output_collection name="correlations" count="5">
80 <element name="0.41.kendall" md5="f01da5dc45d0bae35b692a7306bdc581" ftype="mothur.otu.corr"/>
81 </output_collection>
82 <expand macro="logfile-test"/>
83 </test>
84 </tests>
85 <help>
86 <![CDATA[
87
88 @MOTHUR_OVERVIEW@
89
90 **Command Documentation**
91
92 The otu.association_ command calculates the correlation coefficient for the otus in a shared_ or relabund_ file.
93
94 .. _shared: https://www.mothur.org/wiki/Shared_file
95 .. _relabund: https://www.mothur.org/wiki/Get.relabund
96 .. _otu.association: https://www.mothur.org/wiki/Otu.association
97
98 v.1.25.0: Updated to mothur 1.33, added cutoff option
99 ]]>
100 </help>
101 <expand macro="citations"/>
102 </tool>