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comparison summary.shared.xml @ 1:1a4ad79bc1cd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:36:00 -0400
parents 5c753aec181b
children 2b8970aa8c5c
comparison
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0:5c753aec181b 1:1a4ad79bc1cd
2 <description>Summary of calculator values for OTUs</description> 2 <description>Summary of calculator values 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 'summary.shared( 15 echo 'summary.shared(
13 shared=otu.dat, 16 shared=otu.dat,
35 output=$output, 38 output=$output,
36 processors='\${GALAXY_SLOTS:-8}' 39 processors='\${GALAXY_SLOTS:-8}'
37 )' 40 )'
38 | sed 's/ //g' ## mothur trips over whitespace 41 | sed 's/ //g' ## mothur trips over whitespace
39 | mothur 42 | mothur
43 | tee mothur.out.log
40 ]]></command> 44 ]]></command>
41 <inputs> 45 <inputs>
42 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/> 46 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
43 <param name="label" type="select" label="label - OTU Labels" multiple="true"> 47 <param name="label" type="select" label="label - OTU Labels" multiple="true">
44 <expand macro="labeloptions"/> 48 <expand macro="labeloptions"/>
47 <options> 51 <options>
48 <filter type="data_meta" ref="otu" key="groups"/> 52 <filter type="data_meta" ref="otu" key="groups"/>
49 </options> 53 </options>
50 </param> 54 </param>
51 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> 55 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
56 <expand macro="calc-common"/>
57 <!-- set default option(s) -->
52 <option value="sharedsobs" selected="true">sharedsobs - Shared community richness the observed richness shared between two or more samples</option> 58 <option value="sharedsobs" selected="true">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
53 <option value="sharedchao" selected="true">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option> 59 <option value="sharedchao" selected="true">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
54 <option value="sharedace" selected="true">sharedace - Shared community richness the two sample shared ACE richness estimator</option> 60 <option value="sharedace" selected="true">sharedace - Shared community richness the two sample shared ACE richness estimator</option>
55 <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option>
56 <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option> 61 <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
57 <option value="jest" selected="true">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option> 62 <option value="jest" selected="true">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
58 <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option>
59 <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option>
60 <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option>
61 <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option>
62 <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option>
63 <option value="sorclass" selected="true">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option> 63 <option value="sorclass" selected="true">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
64 <option value="sorest" selected="true">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option> 64 <option value="sorest" selected="true">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
65 <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
66 <option value="hamming">hamming - Community Membership Similarity -</option>
67 <option value="memchi2">memchi2 - Community Membership Similarity -</option>
68 <option value="memchord">memchord - Community Membership Similarity -</option>
69 <option value="memeuclidean">memeuclidean - Community Membership Similarity -</option>
70 <option value="mempearson">mempearson - Community Membership Similarity -</option>
71 <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
72 <option value="jabund" selected="true">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option> 65 <option value="jabund" selected="true">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
73 <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
74 <option value="sorabund" selected="true">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option> 66 <option value="sorabund" selected="true">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
75 <option value="thetan" selected="true">thetan - Community Structure Similarity the Smith theta similarity coefficient</option> 67 <option value="thetan" selected="true">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
76 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option> 68 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
77 <option value="canberra">canberra - Community Structure Similarity -</option>
78 <option value="gower">gower - Community Structure Similarity -</option>
79 <option value="hellinger">hellinger - Community Structure Similarity -</option>
80 <option value="manhattan">manhattan - Community Structure Similarity -</option>
81 <option value="odum">odum - Community Structure Similarity -</option>
82 <option value="soergel">soergel - Community Structure Similarity -</option>
83 <option value="spearman">spearman - Community Structure Similarity -</option>
84 <option value="speciesprofile">speciesprofile - Community Structure Similarity -</option>
85 <option value="structchi2">structchi2 - Community Structure Similarity -</option>
86 <option value="structchord">structchord - Community Structure Similarity -</option>
87 <option value="structeuclidean">structeuclidean - Community Structure Similarity -</option>
88 <option value="structkulczynski">structkulczynski - Community Structure Similarity -</option>
89 <option value="structpearson">structpearson - Community Structure Similarity -</option>
90 <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option>
91 <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option>
92 </param> 69 </param>
93 <param name="all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="all - Include RAM intensive sharedsobs and sharedchao calculations"/> 70 <param name="all" type="boolean" truevalue="true" falsevalue="false" checked="false" label="all - Include RAM intensive sharedsobs and sharedchao calculations"/>
94 <param name="distance" type="boolean" truevalue="true" falsevalue="false" checked="false" label="distance - Output a distance file for each calculator at each label"/> 71 <param name="distance" type="boolean" truevalue="true" falsevalue="false" checked="false" label="distance - Output a distance file for each calculator at each label"/>
95 <conditional name="subsample"> 72 <conditional name="subsample">
96 <param name="use" type="select" label="produce subsample distance matrices"> 73 <param name="use" type="select" label="produce subsample distance matrices">
111 <outputs> 88 <outputs>
112 <expand macro="logfile-output"/> 89 <expand macro="logfile-output"/>
113 <data name="summary" format="tabular" from_work_dir="otu*.summary" label="${tool.name} on ${on_string}: shared.summary"/> 90 <data name="summary" format="tabular" from_work_dir="otu*.summary" label="${tool.name} on ${on_string}: shared.summary"/>
114 <collection name="distfiles" type="list" label="${tool.name} on ${on_string}: dist"> 91 <collection name="distfiles" type="list" label="${tool.name} on ${on_string}: dist">
115 <filter>distance</filter> 92 <filter>distance</filter>
116 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.dist" format="mothur.dist"> 93 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.dist" format="mothur.dist" />
117 <!-- doesn't seem to work for collection elements yet 94 <!-- doesn't seem to work for collection elements yet
118 <change_format> 95 <change_format>
119 <when input="output" value="lt" format="mothur.lower.dist"/> 96 <when input="output" value="lt" format="mothur.lower.dist"/>
120 <when input="output" value="square" format="mothur.square.dist"/> 97 <when input="output" value="square" format="mothur.square.dist"/>
121 </change_format> 98 </change_format>
122 --> 99 -->
123 </discover_datasets>
124 </collection> 100 </collection>
125 </outputs> 101 </outputs>
126 <tests> 102 <tests>
127 <test><!-- test with defaults --> 103 <test><!-- test with defaults -->
128 <param name="otu" value="amazon.an.shared"/> 104 <param name="otu" value="amazon.an.shared"/>
174 <help> 150 <help>
175 <![CDATA[ 151 <![CDATA[
176 152
177 @MOTHUR_OVERVIEW@ 153 @MOTHUR_OVERVIEW@
178 154
179 **Command Documenation** 155 **Command Documentation**
180 156
181 The summary.shared_ command produce a summary file that has the calculator value for each line in the OTU data of the shared_ file and for all possible comparisons between the different groups in the group_ file. This can be useful if you aren't interested in generating collector's or rarefaction curves for your multi-sample data analysis. It would be worth your while, however, to look at the collector's curves for the calculators you are interested in to determine how sensitive the values are to sampling. If the values are not sensitive to sampling, then you can trust the values. Otherwise, you need to keep sampling. For calc parameter choices see: http://www.mothur.org/wiki/Calculators 157 The summary.shared_ command produce a summary file that has the calculator value for each line in the OTU data of the shared_ file and for all possible comparisons between the different groups in the group_ file. This can be useful if you aren't interested in generating collector's or rarefaction curves for your multi-sample data analysis. It would be worth your while, however, to look at the collector's curves for the calculators you are interested in to determine how sensitive the values are to sampling. If the values are not sensitive to sampling, then you can trust the values. Otherwise, you need to keep sampling. For calc parameter choices see: https://www.mothur.org/wiki/Calculators
182 158
183 .. _shared: http://www.mothur.org/wiki/Shared_file 159 .. _shared: https://www.mothur.org/wiki/Shared_file
184 .. _group: http://www.mothur.org/wiki/Group_file 160 .. _group: https://www.mothur.org/wiki/Group_file
185 .. _summary.shared: http://www.mothur.org/wiki/Summary.shared 161 .. _summary.shared: https://www.mothur.org/wiki/Summary.shared
186 ]]> 162 ]]>
187 </help> 163 </help>
188 <expand macro="citations"/> 164 <expand macro="citations"/>
189 </tool> 165 </tool>