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comparison rarefaction.single.xml @ 0:ee20e83b2a92 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 04:54:15 -0400
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children 871f24df79d8
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-1:000000000000 0:ee20e83b2a92
1 <tool profile="16.07" id="mothur_rarefaction_single" name="Rarefaction.single" version="@WRAPPER_VERSION@.0">
2 <description>Generate intra-sample rarefaction 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 'rarefaction.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 iters=$iters,
31 freq=$freq,
32 processors='\${GALAXY_SLOTS:-8}'
33 )'
34 | sed 's/ //g' ## mothur trips over whitespace
35 | mothur
36 | tee mothur.out.log
37
38 ## rename output from sobs calculator to be consistent with others
39 #if 'sobs' in str($calc).split(','):
40 && mv otu\.*rarefaction otu.r_sobs
41 #end if
42 ]]></command>
43 <inputs>
44 <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund,mothur.shared" label="list,rabund,sabund,shared - OTU List"/>
45 <param name="label" type="select" label="label - OTU Labels" multiple="true">
46 <expand macro="labeloptions"/>
47 </param>
48 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
49 <option value="ace">ace - Community richness the ACE estimator</option>
50 <option value="bootstrap">bootstrap - Community richness the bootstrap estimator</option>
51 <option value="chao">chao - Community richness the Chao1 estimator</option>
52 <option value="jack">jack - Community richness the jackknife estimator</option>
53 <option value="sobs" selected="true">sobs - Community richness the observed richness</option>
54 <option value="simpsoneven">simpsoneven - Community evenness a Simpson index-based measure of evenness</option>
55 <option value="shannoneven">shannoneven - Community evenness a Shannon index-based measure of evenness</option>
56 <option value="heip">heip - Community evenness Heip's metric of community evenness</option>
57 <option value="smithwilson">smithwilson - Community evenness Smith and Wilson's metric of community evenness</option>
58 <option value="coverage">coverage - Community diversity the sampling coverage </option>
59 <option value="simpson">simpson - Community diversity the Simpson index</option>
60 <option value="invsimpson">invsimpson - Community diversity the Simpson index</option>
61 <option value="shannon">shannon - Community diversity the Shannon index</option>
62 <option value="npshannon">npshannon - Community diversity the non-parametric Shannon index</option>
63 <option value="nseqs">nseqs - Utility the number of sequences in a sample</option>
64 </param>
65 <param name="abund" type="integer" value="10" min="0" label="abund - ACE Estimator threshold for abundant versus rare OTUs"/>
66 <param name="iters" type="integer" value="1000" min="0" label="iters - Number of randomizations"/>
67 <param name="freq" type="float" value="100" min="0" max="100" label="freq - Reporting frequency" help="if between 0 and 1 the fraction of sequences to sample, if greater than one - report every n iterations"/>
68 </inputs>
69 <outputs>
70 <expand macro="logfile-output"/>
71 <collection name="rarefactioncurves" type="list" label="${tool.name} on ${on_string}: rarefaction curves">
72 <discover_datasets pattern=".*?(\.groups)?\.r_(?P&lt;designation&gt;.*)" format="tabular"/>
73 </collection>
74 </outputs>
75 <tests>
76 <test><!-- test with default values -->
77 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
78 <output_collection name="rarefactioncurves" count="1">
79 <element name="sobs" md5="c4c1f1970edf87ea5103e0704130f079" ftype="tabular"/>
80 </output_collection>
81 <expand macro="logfile-test"/>
82 </test>
83 <test><!-- test with all calculators and subset of labels -->
84 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
85 <param name="calc" value="ace,bootstrap,chao,jack,sobs,simpsoneven,shannoneven,heip,smithwilson,coverage,simpson,invsimpson,shannon,npshannon,nseqs"/>
86 <param name="label" value="0.03,0.05,0.36,0.55"/>
87 <output_collection name="rarefactioncurves" count="15">
88 <element name="simpson" md5="8d6b7ad9a68c30c882e93b17d343042a" ftype="tabular"/>
89 </output_collection>
90 <expand macro="logfile-test"/>
91 </test>
92 </tests>
93 <help>
94 <![CDATA[
95
96 @MOTHUR_OVERVIEW@
97
98 **Command Documentation**
99
100 The rarefaction.single_ command generates intra-sample rarefaction curves using a re-sampling without replacement approach. Rarefaction curves provide a way of comparing the richness observed in different samples. For calc parameter choices see: https://www.mothur.org/wiki/Calculators
101
102 .. _rarefaction.single: https://www.mothur.org/wiki/Rarefaction.single
103 ]]>
104 </help>
105 <expand macro="citations"/>
106 </tool>