Mercurial > repos > iuc > mothur_tree_shared

comparison tree.shared.xml @ 5:466897b7c726 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 14:08:21 -0400
parents 8d6cd6767107
children
comparison
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4:f1bd26502b48 5:466897b7c726
103 <expand macro="calc-common"/> 103 <expand macro="calc-common"/>
104 <!-- set default option(s) --> 104 <!-- set default option(s) -->
105 <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option> 105 <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
106 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option> 106 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
107 </param> 107 </param>
108 <expand macro="param-savelog"/>
108 </inputs> 109 </inputs>
109 <outputs> 110 <outputs>
110 <expand macro="logfile-output"/> 111 <expand macro="logfile-output"/>
111 <data name="tre" format="mothur.tre" from_work_dir="input_dist*.tre" label="${tool.name} on ${on_string}: tre"> 112 <data name="tre" format="mothur.tre" from_work_dir="input_dist*.tre" label="${tool.name} on ${on_string}: tre">
112 <filter>input['source'] != 'shared'</filter> 113 <filter>input['source'] != 'shared'</filter>
119 <tests> 120 <tests>
120 <test><!-- test with phylip and defaults --> 121 <test><!-- test with phylip and defaults -->
121 <param name="source" value="phylip"/> 122 <param name="source" value="phylip"/>
122 <param name="dist" value="env.dist"/> 123 <param name="dist" value="env.dist"/>
123 <output name="tre" md5="c74a88ed448aad2d07059eda0b4161e9" ftype="mothur.tre"/> 124 <output name="tre" md5="c74a88ed448aad2d07059eda0b4161e9" ftype="mothur.tre"/>
125 <param name="savelog" value="true"/>
124 <expand macro="logfile-test"/> 126 <expand macro="logfile-test"/>
125 </test> 127 </test>
126 <test><!-- test with shared and subsampling --> 128 <test><!-- test with shared and subsampling -->
127 <param name="source" value="shared"/> 129 <param name="source" value="shared"/>
128 <param name="dist" value="amazon.an.shared"/> 130 <param name="dist" value="amazon.an.shared"/>
129 <param name="use" value="yes"/> 131 <param name="use" value="yes"/>
130 <param name="calc" value="jclass"/> 132 <param name="calc" value="jclass"/>
131 <output_collection name="trefiles" count="108"> 133 <output_collection name="trefiles" count="108">
132 <element name="jclass.0.32.all" md5="b8adfa6e41397b3815768f987836d102" ftype="mothur.tre"/> 134 <element name="jclass.0.32.all" md5="b8adfa6e41397b3815768f987836d102" ftype="mothur.tre"/>
133 </output_collection> 135 </output_collection>
136 <param name="savelog" value="true"/>
134 <expand macro="logfile-test"/> 137 <expand macro="logfile-test"/>
135 </test> 138 </test>
136 <test><!-- test with shared and label and group select and all calculators --> 139 <test><!-- test with shared and label and group select and all calculators -->
137 <param name="source" value="shared"/> 140 <param name="source" value="shared"/>
138 <param name="dist" value="amazon.an.shared"/> 141 <param name="dist" value="amazon.an.shared"/>
140 <param name="groups" value="forest,pasture"/> 143 <param name="groups" value="forest,pasture"/>
141 <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,sharedobserved"/> 144 <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,sharedobserved"/>
142 <output_collection name="trefiles" count="117"> 145 <output_collection name="trefiles" count="117">
143 <element name="canberra.0.32" md5="477b061d738d24a7476dd4c90d9666cf" ftype="mothur.tre"/> 146 <element name="canberra.0.32" md5="477b061d738d24a7476dd4c90d9666cf" ftype="mothur.tre"/>
144 </output_collection> 147 </output_collection>
148 <param name="savelog" value="true"/>
145 <expand macro="logfile-test"/> 149 <expand macro="logfile-test"/>
146 </test> 150 </test>
147 <test><!-- test with column and name file --> 151 <test><!-- test with column and name file -->
148 <param name="source" value="column"/> 152 <param name="source" value="column"/>
149 <param name="dist" value="amazon.pair.dist"/> 153 <param name="dist" value="amazon.pair.dist"/>
150 <param name="name" value="amazon1.names"/> 154 <param name="name" value="amazon1.names"/>
151 <output name="tre" md5="33cc8cb433f123e49b33b998186b74ed" ftype="mothur.tre"/> 155 <output name="tre" md5="33cc8cb433f123e49b33b998186b74ed" ftype="mothur.tre"/>
156 <param name="savelog" value="true"/>
152 <expand macro="logfile-test"/> 157 <expand macro="logfile-test"/>
153 </test> 158 </test>
154 </tests> 159 </tests>
155 <help><![CDATA[ 160 <help><![CDATA[
156 161