Mercurial > repos > iuc > mothur_otu_association

comparison otu.association.xml @ 2:3c42f300324e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:26:22 -0400
parents 4b4ca5a8e3e2
children 7cfe3ddd183a
comparison
equal deleted inserted replaced
1:435b52e38889 2:3c42f300324e
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$otu" otu.dat && 13 ln -s '$otu' otu.dat &&
14 ln -s "$metadata" metadata.dat && 14 ln -s '$metadata' metadata.dat &&
15 15
16 echo 'otu.association( 16 echo 'otu.association(
17 #if $otu.is_of_type("mothur.relabund"): 17 #if $otu.is_of_type("mothur.relabund"):
18 relabund=otu.dat 18 relabund=otu.dat
19 #elif $otu.is_of_type("mothur.shared"): 19 #elif $otu.is_of_type("mothur.shared"):
20 shared=otu.dat 20 shared=otu.dat
21 #end if 21 #end if
22 #if $label: 22 #if $label:
23 ,label=${ str($label).replace(",","-") } 23 ,label=${ str($label).replace(",","-") }
24 #end if 24 #end if
25 #if $groups: 25 #if $groups:
26 ,groups=${ str($groups).replace(",","-") } 26 ,groups=${ str($groups).replace(",","-") }
27 #end if 27 #end if
28 #if $method: 28 #if $method:
29 ,method=$method 29 ,method=$method
30 #end if 30 #end if
31 #if $metadata: 31 #if $metadata:
32 ,metadata=metadata.dat 32 ,metadata=metadata.dat
33 #end if 33 #end if
34 #if $cutoff: 34 #if $cutoff:
35 ,cutoff=$cutoff 35 ,cutoff=$cutoff
36 #end if 36 #end if
37 )' 37 )'
38 | sed 's/ //g' ## mothur trips over whitespace 38 | sed 's/ //g' ## mothur trips over whitespace
39 | mothur 39 | mothur
40 | tee mothur.out.log 40 | tee mothur.out.log
41 ]]></command> 41 ]]></command>
42 <inputs> 42 <inputs>
43 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/> 43 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/>
44 <param name="label" type="select" label="label - OTU Labels" multiple="true" help="By default all labels are used"> 44 <param name="label" type="select" label="label - OTU Labels" multiple="true" help="By default all labels are used">
45 <expand macro="labeloptions"/> 45 <expand macro="labeloptions"/>
54 <option value="spearman">spearman</option> 54 <option value="spearman">spearman</option>
55 <option value="kendall">kendall</option> 55 <option value="kendall">kendall</option>
56 </param> 56 </param>
57 <param name="metadata" type="data" format="tabular" optional="true" label="metadata - find the association between the otus and the metadata."/> 57 <param name="metadata" type="data" format="tabular" optional="true" label="metadata - find the association between the otus and the metadata."/>
58 <param name="cutoff" type="float" value="" min="0" max="1" optional="true" label="cutoff - set a pvalue at which the otu will be reported"/> 58 <param name="cutoff" type="float" value="" min="0" max="1" optional="true" label="cutoff - set a pvalue at which the otu will be reported"/>
59 <expand macro="param-savelog"/>
59 </inputs> 60 </inputs>
60 <outputs> 61 <outputs>
61 <expand macro="logfile-output"/> 62 <expand macro="logfile-output"/>
62 <collection name="correlations" type="list" label="${tool.name} on ${on_string}: correlation coefficient files per OTU label"> 63 <collection name="correlations" type="list" label="${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 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.otu\.corr" format="mothur.otu.corr"/>
67 <test><!-- test with shared file and default settings --> 68 <test><!-- test with shared file and default settings -->
68 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 69 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
69 <output_collection name="correlations" count="36"> 70 <output_collection name="correlations" count="36">
70 <element name="0.41.pearson" md5="ba93b529a7b0e5ca3baa8fe9a41b4107" ftype="mothur.otu.corr"/> 71 <element name="0.41.pearson" md5="ba93b529a7b0e5ca3baa8fe9a41b4107" ftype="mothur.otu.corr"/>
71 </output_collection> 72 </output_collection>
73 <param name="savelog" value="true"/>
72 <expand macro="logfile-test"/> 74 <expand macro="logfile-test"/>
73 </test> 75 </test>
74 <test><!-- test with relabund file and label and group select --> 76 <test><!-- test with relabund file and label and group select -->
75 <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/> 77 <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/>
76 <param name="method" value="kendall"/> 78 <param name="method" value="kendall"/>
77 <param name="label" value="0.03,0.05,0.36,0.41,0.55"/> 79 <param name="label" value="0.03,0.05,0.36,0.41,0.55"/>
78 <param name="groups" value="forest,pasture"/> 80 <param name="groups" value="forest,pasture"/>
79 <output_collection name="correlations" count="5"> 81 <output_collection name="correlations" count="5">
80 <element name="0.41.kendall" md5="f01da5dc45d0bae35b692a7306bdc581" ftype="mothur.otu.corr"/> 82 <element name="0.41.kendall" md5="f01da5dc45d0bae35b692a7306bdc581" ftype="mothur.otu.corr"/>
81 </output_collection> 83 </output_collection>
84 <param name="savelog" value="true"/>
82 <expand macro="logfile-test"/> 85 <expand macro="logfile-test"/>
83 </test> 86 </test>
84 </tests> 87 </tests>
85 <help> 88 <help><![CDATA[
86 <![CDATA[
87 89
88 @MOTHUR_OVERVIEW@ 90 @MOTHUR_OVERVIEW@
89 91
90 **Command Documentation** 92 **Command Documentation**
91 93
94 .. _shared: https://www.mothur.org/wiki/Shared_file 96 .. _shared: https://www.mothur.org/wiki/Shared_file
95 .. _relabund: https://www.mothur.org/wiki/Get.relabund 97 .. _relabund: https://www.mothur.org/wiki/Get.relabund
96 .. _otu.association: https://www.mothur.org/wiki/Otu.association 98 .. _otu.association: https://www.mothur.org/wiki/Otu.association
97 99
98 v.1.25.0: Updated to mothur 1.33, added cutoff option 100 v.1.25.0: Updated to mothur 1.33, added cutoff option
99 ]]> 101
100 </help> 102 ]]></help>
101 <expand macro="citations"/> 103 <expand macro="citations"/>
102 </tool> 104 </tool>