Mercurial > repos > iuc > mothur_rarefaction_single

comparison rarefaction.single.xml @ 2:871f24df79d8 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 22:07:50 -0400
parents ee20e83b2a92
children 8091da04fbac
comparison
equal deleted inserted replaced
1:62bf570a8a7d 2:871f24df79d8
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 'rarefaction.single( 15 echo 'rarefaction.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=$abund,
30 iters=$iters, 30 iters=$iters,
31 freq=$freq, 31 freq=$freq,
32 processors='\${GALAXY_SLOTS:-8}' 32 processors='\${GALAXY_SLOTS:-8}'
33 )' 33 )'
34 | sed 's/ //g' ## mothur trips over whitespace 34 | sed 's/ //g' ## mothur trips over whitespace
35 | mothur 35 | mothur
36 | tee mothur.out.log 36 | tee mothur.out.log
37 37
38 ## rename output from sobs calculator to be consistent with others 38 ## rename output from sobs calculator to be consistent with others
39 #if 'sobs' in str($calc).split(','): 39 #if 'sobs' in str($calc).split(','):
40 && mv otu\.*rarefaction otu.r_sobs 40 && mv otu\.*rarefaction otu.r_sobs
41 #end if 41 #end if
42 ]]></command> 42 ]]></command>
43 <inputs> 43 <inputs>
44 <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund,mothur.shared" label="list,rabund,sabund,shared - OTU List"/> 44 <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund,mothur.shared" label="list,rabund,sabund,shared - OTU List"/>
45 <param name="label" type="select" label="label - OTU Labels" multiple="true"> 45 <param name="label" type="select" label="label - OTU Labels" multiple="true">
46 <expand macro="labeloptions"/> 46 <expand macro="labeloptions"/>
63 <option value="nseqs">nseqs - Utility the number of sequences in a sample</option> 63 <option value="nseqs">nseqs - Utility the number of sequences in a sample</option>
64 </param> 64 </param>
65 <param name="abund" type="integer" value="10" min="0" label="abund - ACE Estimator threshold for abundant versus rare OTUs"/> 65 <param name="abund" type="integer" value="10" min="0" label="abund - ACE Estimator threshold for abundant versus rare OTUs"/>
66 <param name="iters" type="integer" value="1000" min="0" label="iters - Number of randomizations"/> 66 <param name="iters" type="integer" value="1000" min="0" label="iters - Number of randomizations"/>
67 <param name="freq" type="float" value="100" min="0" max="100" label="freq - Reporting frequency" help="if between 0 and 1 the fraction of sequences to sample, if greater than one - report every n iterations"/> 67 <param name="freq" type="float" value="100" min="0" max="100" label="freq - Reporting frequency" help="if between 0 and 1 the fraction of sequences to sample, if greater than one - report every n iterations"/>
68 <expand macro="param-savelog"/>
68 </inputs> 69 </inputs>
69 <outputs> 70 <outputs>
70 <expand macro="logfile-output"/> 71 <expand macro="logfile-output"/>
71 <collection name="rarefactioncurves" type="list" label="${tool.name} on ${on_string}: rarefaction curves"> 72 <collection name="rarefactioncurves" type="list" label="${tool.name} on ${on_string}: rarefaction curves">
72 <discover_datasets pattern=".*?(\.groups)?\.r_(?P&lt;designation&gt;.*)" format="tabular"/> 73 <discover_datasets pattern=".*?(\.groups)?\.r_(?P&lt;designation&gt;.*)" format="tabular"/>
76 <test><!-- test with default values --> 77 <test><!-- test with default values -->
77 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 78 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
78 <output_collection name="rarefactioncurves" count="1"> 79 <output_collection name="rarefactioncurves" count="1">
79 <element name="sobs" md5="c4c1f1970edf87ea5103e0704130f079" ftype="tabular"/> 80 <element name="sobs" md5="c4c1f1970edf87ea5103e0704130f079" ftype="tabular"/>
80 </output_collection> 81 </output_collection>
82 <param name="savelog" value="true"/>
81 <expand macro="logfile-test"/> 83 <expand macro="logfile-test"/>
82 </test> 84 </test>
83 <test><!-- test with all calculators and subset of labels --> 85 <test><!-- test with all calculators and subset of labels -->
84 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 86 <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"/> 87 <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"/> 88 <param name="label" value="0.03,0.05,0.36,0.55"/>
87 <output_collection name="rarefactioncurves" count="15"> 89 <output_collection name="rarefactioncurves" count="15">
88 <element name="simpson" md5="8d6b7ad9a68c30c882e93b17d343042a" ftype="tabular"/> 90 <element name="simpson" md5="8d6b7ad9a68c30c882e93b17d343042a" ftype="tabular"/>
89 </output_collection> 91 </output_collection>
92 <param name="savelog" value="true"/>
90 <expand macro="logfile-test"/> 93 <expand macro="logfile-test"/>
91 </test> 94 </test>
92 </tests> 95 </tests>
93 <help> 96 <help><![CDATA[
94 <![CDATA[
95 97
96 @MOTHUR_OVERVIEW@ 98 @MOTHUR_OVERVIEW@
97 99
98 **Command Documentation** 100 **Command Documentation**
99 101
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 102 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
101 103
102 .. _rarefaction.single: https://www.mothur.org/wiki/Rarefaction.single 104 .. _rarefaction.single: https://www.mothur.org/wiki/Rarefaction.single
103 ]]> 105
104 </help> 106 ]]></help>
105 <expand macro="citations"/> 107 <expand macro="citations"/>
106 </tool> 108 </tool>