Mercurial > repos > iuc > mothur_collect_shared

comparison collect.shared.xml @ 4:c6684441526a 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 13:47:53 -0400
parents c46d135d6a32
children 1660dae833fe
comparison
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3:c46d135d6a32 4:c6684441526a
56 <option value="thetan" selected="true">thetan - Community Structure Similarity the Smith theta similarity coefficient</option> 56 <option value="thetan" selected="true">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
57 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option> 57 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
58 </param> 58 </param>
59 <param name="freq" type="float" value="100" label="freq - indicates when to output your data" 59 <param name="freq" type="float" value="100" label="freq - indicates when to output your data"
60 help="by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%" min="0.0" max="100.0"/> 60 help="by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%" min="0.0" max="100.0"/>
61 <expand macro="param-savelog"/>
61 </inputs> 62 </inputs>
62 <outputs> 63 <outputs>
63 <expand macro="logfile-output"/> 64 <expand macro="logfile-output"/>
64 <collection name="calcfiles" type="list" label="${tool.name} on ${on_string}: calculators"> 65 <collection name="calcfiles" type="list" label="${tool.name} on ${on_string}: calculators">
65 <discover_datasets pattern="otu\.(?P&lt;designation&gt;.*)" format="tabular"/> 66 <discover_datasets pattern="otu\.(?P&lt;designation&gt;.*)" format="tabular"/>
69 <test><!-- test default settings --> 70 <test><!-- test default settings -->
70 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 71 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
71 <output_collection name="calcfiles" count="11"> 72 <output_collection name="calcfiles" count="11">
72 <element name="jest" md5="22e97fbdbdadf3c4748d0f7c4d526855" ftype="tabular"/> 73 <element name="jest" md5="22e97fbdbdadf3c4748d0f7c4d526855" ftype="tabular"/>
73 </output_collection> 74 </output_collection>
75 <param name="savelog" value="true"/>
74 <expand macro="logfile-test"/> 76 <expand macro="logfile-test"/>
75 </test> 77 </test>
76 <test><!-- test with group and label select and all calculators --> 78 <test><!-- test with group and label select and all calculators -->
77 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 79 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
78 <param name="groups" value="forest,pasture"/> 80 <param name="groups" value="forest,pasture"/>
79 <param name="label" value="0.03,0.05,0.22"/> 81 <param name="label" value="0.03,0.05,0.22"/>
80 <param name="calc" value="sharedsobs,sharedchao,sharedace,anderberg,jclass,jest,kulczynski,kulczynskicody,kstest,lennon,ochiai,sorclass,sorest,whittaker,hamming,memchi2,memchord,memeuclidean,mempearson,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc,canberra,gower,hellinger,manhattan,odum,soergel,spearman,speciesprofile,structchi2,structchord,structeuclidean,structkulczynski,structpearson,sharednseqs"/> 82 <param name="calc" value="sharedsobs,sharedchao,sharedace,anderberg,jclass,jest,kulczynski,kulczynskicody,kstest,lennon,ochiai,sorclass,sorest,whittaker,hamming,memchi2,memchord,memeuclidean,mempearson,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc,canberra,gower,hellinger,manhattan,odum,soergel,spearman,speciesprofile,structchi2,structchord,structeuclidean,structkulczynski,structpearson,sharednseqs"/>
81 <output_collection name="calcfiles" count="39"> 83 <output_collection name="calcfiles" count="39">
82 <element name="jest" md5="1289eac7fdcfb42eaf4ee35deb6fb0a4" ftype="tabular"/> 84 <element name="jest" md5="1289eac7fdcfb42eaf4ee35deb6fb0a4" ftype="tabular"/>
83 </output_collection> 85 </output_collection>
86 <param name="savelog" value="true"/>
84 <expand macro="logfile-test"/> 87 <expand macro="logfile-test"/>
85 </test> 88 </test>
86 </tests> 89 </tests>
87 <help><![CDATA[ 90 <help><![CDATA[
88 91