Mercurial > repos > iuc > mothur_rarefaction_single

comparison rarefaction.single.xml @ 1:3779e72d3525 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:52:12 -0400
parents 4e53dc9d5e83
children 5fa888231577
comparison
equal deleted inserted replaced
0:4e53dc9d5e83 1:3779e72d3525
2 <description>Generate intra-sample rarefaction curves for OTUs</description> 2 <description>Generate intra-sample rarefaction curves for OTUs</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
9 ## create symlinks to input datasets 12 ## create symlinks to input datasets
10 ln -s "$otu" otu.dat && 13 ln -s "$otu" otu.dat &&
11 14
12 echo 'rarefaction.single( 15 echo 'rarefaction.single(
13 #if $otu.is_of_type("mothur.rabund"): 16 #if $otu.is_of_type("mothur.rabund"):
28 freq=$freq, 31 freq=$freq,
29 processors='\${GALAXY_SLOTS:-8}' 32 processors='\${GALAXY_SLOTS:-8}'
30 )' 33 )'
31 | sed 's/ //g' ## mothur trips over whitespace 34 | sed 's/ //g' ## mothur trips over whitespace
32 | mothur 35 | mothur
36 | tee mothur.out.log
37
38 ## rename output from sobs calculator to be consistent with others
39 #if 'sobs' in str($calc).split(','):
40 && mv otu\.*rarefaction otu.r_sobs
41 #end if
33 ]]></command> 42 ]]></command>
34 <inputs> 43 <inputs>
35 <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"/>
36 <param name="label" type="select" label="label - OTU Labels" multiple="true"> 45 <param name="label" type="select" label="label - OTU Labels" multiple="true">
37 <expand macro="labeloptions"/> 46 <expand macro="labeloptions"/>
58 <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"/>
59 </inputs> 68 </inputs>
60 <outputs> 69 <outputs>
61 <expand macro="logfile-output"/> 70 <expand macro="logfile-output"/>
62 <collection name="rarefactioncurves" type="list" label="${tool.name} on ${on_string}: rarefaction curves"> 71 <collection name="rarefactioncurves" type="list" label="${tool.name} on ${on_string}: rarefaction curves">
63 <discover_datasets pattern=".*?\.groups\.(?P&lt;designation&gt;.*)" format="tabular"/> 72 <discover_datasets pattern=".*?(\.groups)?\.r_(?P&lt;designation&gt;.*)" format="tabular"/>
64 </collection> 73 </collection>
65 </outputs> 74 </outputs>
66 <tests> 75 <tests>
67 <test><!-- test with default values --> 76 <test><!-- test with default values -->
68 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 77 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
69 <output_collection name="rarefactioncurves" count="1"> 78 <output_collection name="rarefactioncurves" count="1">
70 <element name="rarefaction" md5="c4c1f1970edf87ea5103e0704130f079" ftype="tabular"/> 79 <element name="sobs" md5="c4c1f1970edf87ea5103e0704130f079" ftype="tabular"/>
71 </output_collection> 80 </output_collection>
72 <expand macro="logfile-test"/> 81 <expand macro="logfile-test"/>
73 </test> 82 </test>
74 <test><!-- test with all calculators and subset of labels --> 83 <test><!-- test with all calculators and subset of labels -->
75 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 84 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
76 <param name="calc" value="ace,bootstrap,chao,jack,sobs,simpsoneven,shannoneven,heip,smithwilson,coverage,simpson,invsimpson,shannon,npshannon,nseqs"/> 85 <param name="calc" value="ace,bootstrap,chao,jack,sobs,simpsoneven,shannoneven,heip,smithwilson,coverage,simpson,invsimpson,shannon,npshannon,nseqs"/>
77 <param name="label" value="0.03,0.05,0.36,0.55"/> 86 <param name="label" value="0.03,0.05,0.36,0.55"/>
78 <output_collection name="rarefactioncurves" count="15"> 87 <output_collection name="rarefactioncurves" count="15">
79 <element name="r_simpson" md5="8d6b7ad9a68c30c882e93b17d343042a" ftype="tabular"/> 88 <element name="simpson" md5="8d6b7ad9a68c30c882e93b17d343042a" ftype="tabular"/>
80 </output_collection> 89 </output_collection>
81 <expand macro="logfile-test"/> 90 <expand macro="logfile-test"/>
82 </test> 91 </test>
83 </tests> 92 </tests>
84 <help> 93 <help>
85 <![CDATA[ 94 <![CDATA[
86 95
87 @MOTHUR_OVERVIEW@ 96 @MOTHUR_OVERVIEW@
88 97
89 **Command Documenation** 98 **Command Documentation**
90 99
91 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: http://www.mothur.org/wiki/Calculators 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
92 101
93 .. _rarefaction.single: http://www.mothur.org/wiki/Rarefaction.single 102 .. _rarefaction.single: https://www.mothur.org/wiki/Rarefaction.single
94 ]]> 103 ]]>
95 </help> 104 </help>
96 <expand macro="citations"/> 105 <expand macro="citations"/>
97 </tool> 106 </tool>