Mercurial > repos > iuc > mothur_rarefaction_single

comparison rarefaction.single.xml @ 7:b474d518665c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 38a2bbee32eaaceeb22d7549b13dbc0c613ee173
author iuc
date Tue, 20 Mar 2018 13:49:53 -0400
parents 5fa888231577
children 8ccd6a1a7ff8
comparison
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6:ddadbbb71de8 7:b474d518665c
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><![CDATA[ 96 <help><![CDATA[
94 97