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comparison summary.shared.xml @ 3:2b8970aa8c5c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:13:21 -0500
parents 1a4ad79bc1cd
children d98918707cbc
comparison
equal deleted inserted replaced
2:978f77d2117b 3:2b8970aa8c5c
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 14
15 echo 'summary.shared( 15 echo 'summary.shared(
16 shared=otu.dat, 16 shared=otu.dat,
17 #if $groups: 17 #if $groups:
18 label=${ str($label).replace(",","-") }, 18 label=${ str($label).replace(",","-") },
19 #end if 19 #end if
20 #if $label: 20 #if $label:
21 groups=${ str($groups).replace(",","-") }, 21 groups=${ str($groups).replace(",","-") },
22 #end if 22 #end if
23 #if $calc: 23 #if $calc:
24 calc=${ str($calc).replace(",","-") }, 24 calc=${ str($calc).replace(",","-") },
25 #end if 25 #end if
26 all=$all, 26 all=$all,
27 distance=$distance, 27 distance=$distance,
28 #if $subsample.use == "yes": 28 #if $subsample.use == "yes":
29 #if $subsample.subsample: 29 #if $subsample.subsample:
30 subsample=$subsample.subsample, 30 subsample=$subsample.subsample,
31 #else 31 #else
32 subsample=T, 32 subsample=T,
33 #end if 33 #end if
34 #if $subsample.iters: 34 #if $subsample.iters:
35 iters=$subsample.iters, 35 iters=$subsample.iters,
36 #end if 36 #end if
37 #end if 37 #end if
38 output=$output, 38 output=$output,
39 processors='\${GALAXY_SLOTS:-8}' 39 processors='\${GALAXY_SLOTS:-8}'
40 )' 40 )'
41 | sed 's/ //g' ## mothur trips over whitespace 41 | sed 's/ //g' ## mothur trips over whitespace
42 | mothur 42 | mothur
43 | tee mothur.out.log 43 | tee mothur.out.log
44 ]]></command> 44 ]]></command>
45 <inputs> 45 <inputs>
46 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/> 46 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
47 <param name="label" type="select" label="label - OTU Labels" multiple="true"> 47 <param name="label" type="select" label="label - OTU Labels" multiple="true">
48 <expand macro="labeloptions"/> 48 <expand macro="labeloptions"/>
104 <param name="otu" value="amazon.an.shared"/> 104 <param name="otu" value="amazon.an.shared"/>
105 <output name="summary" md5="29384359e341721b3519fba35b9301e4" ftype="tabular"/> 105 <output name="summary" md5="29384359e341721b3519fba35b9301e4" ftype="tabular"/>
106 <expand macro="logfile-test"/> 106 <expand macro="logfile-test"/>
107 </test> 107 </test>
108 <test><!-- test with subsample --> 108 <test><!-- test with subsample -->
109 <param name="otu" value="amazon.an.shared"/> 109 <param name="otu" value="amazon.mothur.shared"/>
110 <param name="use" value="yes"/> 110 <param name="use" value="yes"/>
111 <param name="subsample" value="10"/> 111 <param name="subsample" value="10"/>
112 <param name="iters" value="42"/> 112 <param name="iters" value="42"/>
113 <output name="summary" ftype="tabular"> 113 <output name="summary" ftype="tabular">
114 <assert_contents> 114 <assert_contents>
145 </element> 145 </element>
146 </output_collection> 146 </output_collection>
147 <expand macro="logfile-test"/> 147 <expand macro="logfile-test"/>
148 </test> 148 </test>
149 </tests> 149 </tests>
150 <help> 150 <help><![CDATA[
151 <![CDATA[
152 151
153 @MOTHUR_OVERVIEW@ 152 @MOTHUR_OVERVIEW@
154 153
155 **Command Documentation** 154 **Command Documentation**
156 155
157 The summary.shared_ command produce a summary file that has the calculator value for each line in the OTU data of the shared_ file and for all possible comparisons between the different groups in the group_ file. This can be useful if you aren't interested in generating collector's or rarefaction curves for your multi-sample data analysis. It would be worth your while, however, to look at the collector's curves for the calculators you are interested in to determine how sensitive the values are to sampling. If the values are not sensitive to sampling, then you can trust the values. Otherwise, you need to keep sampling. For calc parameter choices see: https://www.mothur.org/wiki/Calculators 156 The summary.shared_ command produce a summary file that has the calculator value for each line in the OTU data of the shared_ file and for all possible comparisons between the different groups in the group_ file. This can be useful if you aren't interested in generating collector's or rarefaction curves for your multi-sample data analysis. It would be worth your while, however, to look at the collector's curves for the calculators you are interested in to determine how sensitive the values are to sampling. If the values are not sensitive to sampling, then you can trust the values. Otherwise, you need to keep sampling. For calc parameter choices see: https://www.mothur.org/wiki/Calculators
158 157
159 .. _shared: https://www.mothur.org/wiki/Shared_file 158 .. _shared: https://www.mothur.org/wiki/Shared_file
160 .. _group: https://www.mothur.org/wiki/Group_file 159 .. _group: https://www.mothur.org/wiki/Group_file
161 .. _summary.shared: https://www.mothur.org/wiki/Summary.shared 160 .. _summary.shared: https://www.mothur.org/wiki/Summary.shared
162 ]]> 161
163 </help> 162 ]]></help>
164 <expand macro="citations"/> 163 <expand macro="citations"/>
165 </tool> 164 </tool>