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comparison tree.shared.xml @ 1:a16c10c1c418 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 04:33:57 -0400
parents 75c9bf79f50e
children 8d6cd6767107
comparison
equal deleted inserted replaced
0:75c9bf79f50e 1:a16c10c1c418
2 <description>Generate a newick tree for dissimilarity among groups</description> 2 <description>Generate a newick tree for dissimilarity among groups</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 "$input.dist" input_dist.dat && 13 ln -s "$input.dist" input_dist.dat &&
11 #if not $input.source == "shared": 14 #if not $input.source == "shared":
12 ln -s "$input.name" input_name.dat && 15 ln -s "$input.name" input_name.dat &&
13 #end if 16 #end if
47 #end if 50 #end if
48 processors='\${GALAXY_SLOTS:-8}' 51 processors='\${GALAXY_SLOTS:-8}'
49 )' 52 )'
50 | sed 's/ //g' ## mothur trips over whitespace 53 | sed 's/ //g' ## mothur trips over whitespace
51 | mothur 54 | mothur
55 | tee mothur.out.log
52 ]]></command> 56 ]]></command>
53 <inputs> 57 <inputs>
54 <conditional name="input"> 58 <conditional name="input">
55 <param name="source" type="select" label="Select input format"> 59 <param name="source" type="select" label="Select input format">
56 <option value="shared">OTU Shared</option> 60 <option value="shared">OTU Shared</option>
61 <when value="column"> 65 <when value="column">
62 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/> 66 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
63 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/> 67 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
64 </when> 68 </when>
65 <when value="phylip"> 69 <when value="phylip">
66 <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> 70 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
67 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/> 71 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/>
68 </when> 72 </when>
69 <when value="shared"> 73 <when value="shared">
70 <param name="dist" type="data" format="mothur.shared" label="shared - OTU Shared"/> 74 <param name="dist" type="data" format="mothur.shared" label="shared - OTU Shared"/>
71 <param name="label" type="select" label="label - OTU Labels" multiple="true"> 75 <param name="label" type="select" label="label - OTU Labels" multiple="true">
94 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/> 98 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
95 <param name="name" type="data" format="mothur.count_table" label="count - count_table file"/> 99 <param name="name" type="data" format="mothur.count_table" label="count - count_table file"/>
96 </when> 100 </when>
97 </conditional> 101 </conditional>
98 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> 102 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
99 <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option> 103 <expand macro="calc-common"/>
100 <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option> 104 <!-- set default option(s) -->
101 <option value="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</option>
102 <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option>
103 <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>
104 <option value="jest">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
105 <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option>
106 <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option>
107 <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option>
108 <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option>
109 <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option>
110 <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
111 <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
112 <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
113 <option value="hamming">hamming - Community Membership Similarity -</option>
114 <option value="memchi2">memchi2 - Community Membership Similarity -</option>
115 <option value="memchord">memchord - Community Membership Similarity -</option>
116 <option value="memeuclidean">memeuclidean - Community Membership Similarity -</option>
117 <option value="mempearson">mempearson - Community Membership Similarity -</option>
118 <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
119 <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
120 <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
121 <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
122 <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
123 <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>
124 <option value="canberra">canberra - Community Structure Similarity -</option>
125 <option value="gower">gower - Community Structure Similarity -</option>
126 <option value="hellinger">hellinger - Community Structure Similarity -</option>
127 <option value="manhattan">manhattan - Community Structure Similarity -</option>
128 <option value="odum">odum - Community Structure Similarity -</option>
129 <option value="soergel">soergel - Community Structure Similarity -</option>
130 <option value="spearman">spearman - Community Structure Similarity -</option>
131 <option value="speciesprofile">speciesprofile - Community Structure Similarity -</option>
132 <option value="structchi2">structchi2 - Community Structure Similarity -</option>
133 <option value="structchord">structchord - Community Structure Similarity -</option>
134 <option value="structeuclidean">structeuclidean - Community Structure Similarity -</option>
135 <option value="structkulczynski">structkulczynski - Community Structure Similarity -</option>
136 <option value="structpearson">structpearson - Community Structure Similarity -</option>
137 <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option>
138 <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option>
139 </param> 107 </param>
140 </inputs> 108 </inputs>
141 <outputs> 109 <outputs>
142 <expand macro="logfile-output"/> 110 <expand macro="logfile-output"/>
143 <data name="tre" format="mothur.tre" from_work_dir="input_dist*.tre" label="${tool.name} on ${on_string}: tre"> 111 <data name="tre" format="mothur.tre" from_work_dir="input_dist*.tre" label="${tool.name} on ${on_string}: tre">
187 <help> 155 <help>
188 <![CDATA[ 156 <![CDATA[
189 157
190 @MOTHUR_OVERVIEW@ 158 @MOTHUR_OVERVIEW@
191 159
192 **Command Documenation** 160 **Command Documentation**
193 161
194 The tree.shared_ command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups. For calc parameter choices see: http://www.mothur.org/wiki/Calculators 162 The tree.shared_ command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups. For calc parameter choices see: https://www.mothur.org/wiki/Calculators
195 163
196 .. _tree.shared: http://www.mothur.org/wiki/Tree.shared 164 .. _tree.shared: https://www.mothur.org/wiki/Tree.shared
197 165
198 ]]> 166 ]]>
199 </help> 167 </help>
200 <expand macro="citations"/> 168 <expand macro="citations"/>
201 </tool> 169 </tool>