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comparison collect.single.xml @ 0:5996c4d331bc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:17:32 -0400
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children 287b6646d047
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-1:000000000000 0:5996c4d331bc
1 <tool profile="16.07" id="mothur_collect_single" name="Collect.single" version="@WRAPPER_VERSION@.0">
2 <description>Generate collector's curves for 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
15 echo 'collect.single(
16 #if $otu.is_of_type("mothur.rabund"):
17 rabund=otu.dat,
18 #elif $otu.is_of_type("mothur.sabund"):
19 sabund=otu.dat,
20 #elif $otu.is_of_type("mothur.shared"):
21 shared=otu.dat,
22 #elif $otu.is_of_type("mothur.list"):
23 list=otu.dat,
24 #end if
25 #if $label:
26 label=${ str($label).replace(",","-") },
27 #end if
28 calc=${ str($calc).replace(",","-") },
29 abund=$abund,
30 freq=$freq
31 )'
32 | sed 's/ //g' ## mothur trips over whitespace
33 | mothur
34 | tee mothur.out.log
35 && rm otu.dat ## don't want this collected into datacollection
36 ]]></command>
37 <inputs>
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">
40 <expand macro="labeloptions"/>
41 </param>
42 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
43 <option value="ace" selected="true">ace - Community richness the ACE estimator</option>
44 <option value="bootstrap">bootstrap - Community richness the bootstrap estimator</option>
45 <option value="chao" selected="true">chao - Community richness the Chao1 estimator</option>
46 <option value="jack" selected="true">jack - Community richness the jackknife estimator</option>
47 <option value="sobs" selected="true">sobs - Community richness the observed richness</option>
48 <option value="simpsoneven">simpsoneven - Community evenness a Simpson index-based measure of evenness</option>
49 <option value="shannoneven">shannoneven - Community evenness a Shannon index-based measure of evenness</option>
50 <option value="heip">heip - Community evenness Heip's metric of community evenness</option>
51 <option value="smithwilson">smithwilson - Community evenness Smith and Wilson's metric of community evenness</option>
52 <option value="bergerparker">bergerparker - Community diversity the Berger-Parker index</option>
53 <option value="coverage">coverage - Community diversity the sampling coverage </option>
54 <option value="goodscoverage">goodscoverage - Community diversity the Good's estimate of sampling coverage </option>
55 <option value="simpson" selected="true">simpson - Community diversity the Simpson index</option>
56 <option value="invsimpson">invsimpson - Community diversity the Simpson index</option>
57 <option value="qstat">qstat - Community diversity the Q statistic</option>
58 <option value="shannon" selected="true">shannon - Community diversity the Shannon index</option>
59 <option value="npshannon" selected="true">npshannon - Community diversity the non-parametric Shannon index</option>
60 <option value="boneh">boneh - Estimator Boneh's estimator</option>
61 <option value="efron">efron - Estimator Efron's estimator</option>
62 <option value="shen">shen - Estimator Shen's estimator</option>
63 <option value="solow">solow - Estimator Solow's estimator</option>
64 <option value="logseries">logseries - Statistical distribution tests whether observed data follow the log 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>
67 <option value="nseqs">nseqs - Utility the number of sequences in a sample</option>
68 </param>
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"/>
71 </inputs>
72 <outputs>
73 <expand macro="logfile-output"/>
74 <collection name="calcfiles" type="list" label="${tool.name} on ${on_string}: calculators">
75 <discover_datasets pattern="otu\.(?P&lt;designation&gt;.*)" format="tabular"/>
76 </collection>
77 </outputs>
78 <tests>
79 <test><!-- test default settings -->
80 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
81 <output_collection name="calcfiles" count="7">
82 <element name="shannon" md5="0a9c8a52f89898c3b7b7b2dfa24a4521" ftype="tabular"/>
83 </output_collection>
84 <expand macro="logfile-test"/>
85 </test>
86 <test><!-- test with label select and all calculators -->
87 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
88 <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"/>
90 <output_collection name="calcfiles" count="25">
91 <element name="bstick" md5="a38d430c52768efca597e5b41fc1d84b" ftype="tabular"/>
92 </output_collection>
93 <expand macro="logfile-test"/>
94 </test>
95 </tests>
96 <help>
97 <![CDATA[
98
99 @MOTHUR_OVERVIEW@
100
101
102 **Command Documentation**
103
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
105
106 .. _calculators: https://www.mothur.org/wiki/Calculators
107 .. _collect.single: https://www.mothur.org/wiki/Collect.single
108 ]]>
109 </help>
110 <expand macro="citations"/>
111 </tool>