Mercurial > repos > iuc > mothur_collect_single

comparison collect.single.xml @ 2:287b6646d047 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 22:25:10 -0400
parents 5996c4d331bc
children 7f212a2a4a3b
comparison
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1:f9b8cabd4365 2:287b6646d047
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 'collect.single( 15 echo 'collect.single(
16 #if $otu.is_of_type("mothur.rabund"): 16 #if $otu.is_of_type("mothur.rabund"):
17 rabund=otu.dat, 17 rabund=otu.dat,
18 #elif $otu.is_of_type("mothur.sabund"): 18 #elif $otu.is_of_type("mothur.sabund"):
19 sabund=otu.dat, 19 sabund=otu.dat,
20 #elif $otu.is_of_type("mothur.shared"): 20 #elif $otu.is_of_type("mothur.shared"):
21 shared=otu.dat, 21 shared=otu.dat,
22 #elif $otu.is_of_type("mothur.list"): 22 #elif $otu.is_of_type("mothur.list"):
23 list=otu.dat, 23 list=otu.dat,
24 #end if 24 #end if
25 #if $label: 25 #if $label:
26 label=${ str($label).replace(",","-") }, 26 label=${ str($label).replace(",","-") },
27 #end if 27 #end if
28 calc=${ str($calc).replace(",","-") }, 28 calc=${ str($calc).replace(",","-") },
29 abund=$abund, 29 abund=$abund,
30 freq=$freq 30 freq=$freq
31 )' 31 )'
32 | sed 's/ //g' ## mothur trips over whitespace 32 | sed 's/ //g' ## mothur trips over whitespace
33 | mothur 33 | mothur
34 | tee mothur.out.log 34 | tee mothur.out.log
35 && rm otu.dat ## don't want this collected into datacollection 35 && rm otu.dat ## don't want this collected into datacollection
36 ]]></command> 36 ]]></command>
37 <inputs> 37 <inputs>
38 <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund,mothur.shared" label="list,rabund,sabund,shared - OTU List"/> 38 <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund,mothur.shared" label="list,rabund,sabund,shared - OTU List"/>
39 <param name="label" type="select" label="label - OTU Labels" multiple="true"> 39 <param name="label" type="select" label="label - OTU Labels" multiple="true">
40 <expand macro="labeloptions"/> 40 <expand macro="labeloptions"/>
65 <option value="geometric">geometric - Statistical distribution tests whether observed data follow the geometric series distribution</option> 65 <option value="geometric">geometric - Statistical distribution tests whether observed data follow the geometric series distribution</option>
66 <option value="bstick">bstick - Statistical distribution tests whether observed data follow the broken stick distribution</option> 66 <option value="bstick">bstick - Statistical distribution tests whether observed data follow the broken stick distribution</option>
67 <option value="nseqs">nseqs - Utility the number of sequences in a sample</option> 67 <option value="nseqs">nseqs - Utility the number of sequences in a sample</option>
68 </param> 68 </param>
69 <param name="abund" type="integer" value="10" min="0" label="abund - ACE Estimator threshold for abundant versus rare OTUs (default 10)"/> 69 <param name="abund" type="integer" value="10" min="0" label="abund - ACE Estimator threshold for abundant versus rare OTUs (default 10)"/>
70 <param name="freq" type="float" value="100" min="0" label="freq - frequency for output (default is every 100 sequences)" help="Use a decimal between 0 and 1 to set the frequency as a percentage of the number of sequences"/> 70 <param name="freq" type="float" value="100" min="0" label="freq - frequency for output (default is every 100 sequences)"
71 help="Use a decimal between 0 and 1 to set the frequency as a percentage of the number of sequences"/>
72 <expand macro="param-savelog"/>
71 </inputs> 73 </inputs>
72 <outputs> 74 <outputs>
73 <expand macro="logfile-output"/> 75 <expand macro="logfile-output"/>
74 <collection name="calcfiles" type="list" label="${tool.name} on ${on_string}: calculators"> 76 <collection name="calcfiles" type="list" label="${tool.name} on ${on_string}: calculators">
75 <discover_datasets pattern="otu\.(?P&lt;designation&gt;.*)" format="tabular"/> 77 <discover_datasets pattern="otu\.(?P&lt;designation&gt;.*)" format="tabular"/>
79 <test><!-- test default settings --> 81 <test><!-- test default settings -->
80 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 82 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
81 <output_collection name="calcfiles" count="7"> 83 <output_collection name="calcfiles" count="7">
82 <element name="shannon" md5="0a9c8a52f89898c3b7b7b2dfa24a4521" ftype="tabular"/> 84 <element name="shannon" md5="0a9c8a52f89898c3b7b7b2dfa24a4521" ftype="tabular"/>
83 </output_collection> 85 </output_collection>
86 <param name="savelog" value="true"/>
84 <expand macro="logfile-test"/> 87 <expand macro="logfile-test"/>
85 </test> 88 </test>
86 <test><!-- test with label select and all calculators --> 89 <test><!-- test with label select and all calculators -->
87 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/> 90 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
88 <param name="label" value="0.36,0.38,0.41"/> 91 <param name="label" value="0.36,0.38,0.41"/>
89 <param name="calc" value="ace,bootstrap,chao,jack,sobs,simpsoneven,shannoneven,heip,smithwilson,bergerparker,coverage,goodscoverage,simpson,invsimpson,qstat,shannon,npshannon,boneh,efron,shen,solow,logseries,geometric,bstick,nseqs"/> 92 <param name="calc" value="ace,bootstrap,chao,jack,sobs,simpsoneven,shannoneven,heip,smithwilson,bergerparker,coverage,goodscoverage,simpson,invsimpson,qstat,shannon,npshannon,boneh,efron,shen,solow,logseries,geometric,bstick,nseqs"/>
90 <output_collection name="calcfiles" count="25"> 93 <output_collection name="calcfiles" count="25">
91 <element name="bstick" md5="a38d430c52768efca597e5b41fc1d84b" ftype="tabular"/> 94 <element name="bstick" md5="a38d430c52768efca597e5b41fc1d84b" ftype="tabular"/>
92 </output_collection> 95 </output_collection>
96 <param name="savelog" value="true"/>
93 <expand macro="logfile-test"/> 97 <expand macro="logfile-test"/>
94 </test> 98 </test>
95 </tests> 99 </tests>
96 <help> 100 <help><![CDATA[
97 <![CDATA[
98 101
99 @MOTHUR_OVERVIEW@ 102 @MOTHUR_OVERVIEW@
100 103
101 104
102 **Command Documentation** 105 **Command Documentation**
103 106
104 The collect.single_ command generates collector's curves using calculators_, that describe the richness, diversity, and other features of individual samples. Collector's curves describe how richness or diversity change as you sample additional individuals. If a collector's curve becomes parallel to the x-axis, you can be reasonably confident that you have done a good job of sampling and can trust the last value in the curve. Otherwise, you need to keep sampling. For calc parameter choices see: https://www.mothur.org/wiki/Calculators 107 The collect.single_ command generates collector's curves using calculators_, that describe the richness, diversity, and other features of individual samples. Collector's curves describe how richness or diversity change as you sample additional individuals. If a collector's curve becomes parallel to the x-axis, you can be reasonably confident that you have done a good job of sampling and can trust the last value in the curve. Otherwise, you need to keep sampling. For calc parameter choices see: https://www.mothur.org/wiki/Calculators
105 108
106 .. _calculators: https://www.mothur.org/wiki/Calculators 109 .. _calculators: https://www.mothur.org/wiki/Calculators
107 .. _collect.single: https://www.mothur.org/wiki/Collect.single 110 .. _collect.single: https://www.mothur.org/wiki/Collect.single
108 ]]> 111
109 </help> 112 ]]></help>
110 <expand macro="citations"/> 113 <expand macro="citations"/>
111 </tool> 114 </tool>