Mercurial > repos > iuc > mothur_tree_shared

comparison tree.shared.xml @ 0:75c9bf79f50e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:53:03 -0400
parents
children a16c10c1c418
comparison
equal deleted inserted replaced
-1:000000000000 0:75c9bf79f50e
1 <tool profile="16.07" id="mothur_tree_shared" name="Tree.shared" version="@WRAPPER_VERSION@.0">
2 <description>Generate a newick tree for dissimilarity among groups</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$input.dist" input_dist.dat &&
11 #if not $input.source == "shared":
12 ln -s "$input.name" input_name.dat &&
13 #end if
14
15 echo 'tree.shared(
16 #if $input.source == "shared":
17 shared=input_dist.dat,
18 #if $input.groups:
19 groups=${ str($input.groups).replace(",","-") },
20 #end if
21 #if $input.label:
22 label=${ str($input.label).replace(",","-") },
23 #end if
24 #if $input.subsampling.use == "yes":
25 #if $input.subsampling.subsample:
26 subsample=$input.subsampling.subsample,
27 #else
28 subsample=T,
29 #end if
30 #if $input.subsampling.iters:
31 iters="$input.subsampling.iters,
32 #end if
33 #end if
34 #elif $input.source == "column":
35 column=input_dist.dat,
36 name=input_name.dat,
37 #elif $input.source == "phylip":
38 phylip=input_dist.dat,
39 #if $input.name:
40 name=input_name.dat,
41 #end if
42 #else
43 count=input_name.dat,
44 #end if
45 #if $calc:
46 calc=${ str($calc).replace(",","-") },
47 #end if
48 processors='\${GALAXY_SLOTS:-8}'
49 )'
50 | sed 's/ //g' ## mothur trips over whitespace
51 | mothur
52 ]]></command>
53 <inputs>
54 <conditional name="input">
55 <param name="source" type="select" label="Select input format">
56 <option value="shared">OTU Shared</option>
57 <option value="column">Pairwise Column Distance Matrix</option>
58 <option value="phylip">Phylip Distance Matrix</option>
59 <option value="count">Count file</option>
60 </param>
61 <when value="column">
62 <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"/>
64 </when>
65 <when value="phylip">
66 <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
67 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/>
68 </when>
69 <when value="shared">
70 <param name="dist" type="data" format="mothur.shared" label="shared - OTU Shared"/>
71 <param name="label" type="select" label="label - OTU Labels" multiple="true">
72 <options>
73 <filter type="data_meta" ref="dist" key="labels"/>
74 </options>
75 </param>
76 <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
77 <options>
78 <filter type="data_meta" ref="dist" key="groups"/>
79 </options>
80 </param>
81 <conditional name="subsampling">
82 <param name="use" type="select" label="subsample">
83 <option value="no" selected="true">no</option>
84 <option value="yes">yes</option>
85 </param>
86 <when value="yes">
87 <param name="subsample" type="integer" value="" min="0" optional="true" label="subsample (defaults to the size of the smallest group)" help="Should not exceed the number of sequences in any group"/>
88 <param name="iters" type="integer" value="" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/>
89 </when>
90 <when value="no"/>
91 </conditional>
92 </when>
93 <when value="count">
94 <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"/>
96 </when>
97 </conditional>
98 <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>
100 <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
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>
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>
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>
140 </inputs>
141 <outputs>
142 <expand macro="logfile-output"/>
143 <data name="tre" format="mothur.tre" from_work_dir="input_dist*.tre" label="${tool.name} on ${on_string}: tre">
144 <filter>input['source'] != 'shared'</filter>
145 </data>
146 <collection name="trefiles" type="list" label="${tool.name} on ${on_string}: tre">
147 <filter>input['source'] == 'shared'</filter>
148 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.tre" format="mothur.tre"/>
149 </collection>
150 </outputs>
151 <tests>
152 <test><!-- test with phylip and defaults -->
153 <param name="source" value="phylip"/>
154 <param name="dist" value="env.dist"/>
155 <output name="tre" md5="c74a88ed448aad2d07059eda0b4161e9" ftype="mothur.tre"/>
156 <expand macro="logfile-test"/>
157 </test>
158 <test><!-- test with shared and subsampling -->
159 <param name="source" value="shared"/>
160 <param name="dist" value="amazon.an.shared"/>
161 <param name="use" value="yes"/>
162 <param name="calc" value="jclass"/>
163 <output_collection name="trefiles" count="108">
164 <element name="jclass.0.32.all" md5="b8adfa6e41397b3815768f987836d102" ftype="mothur.tre"/>
165 </output_collection>
166 <expand macro="logfile-test"/>
167 </test>
168 <test><!-- test with shared and label and group select and all calculators -->
169 <param name="source" value="shared"/>
170 <param name="dist" value="amazon.an.shared"/>
171 <param name="label" value="0.05,0.22,0.32"/>
172 <param name="groups" value="forest,pasture"/>
173 <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"/>
174 <output_collection name="trefiles" count="117">
175 <element name="canberra.0.32" md5="477b061d738d24a7476dd4c90d9666cf" ftype="mothur.tre"/>
176 </output_collection>
177 <expand macro="logfile-test"/>
178 </test>
179 <test><!-- test with column and name file -->
180 <param name="source" value="column"/>
181 <param name="dist" value="amazon.pair.dist"/>
182 <param name="name" value="amazon1.names"/>
183 <output name="tre" md5="33cc8cb433f123e49b33b998186b74ed" ftype="mothur.tre"/>
184 <expand macro="logfile-test"/>
185 </test>
186 </tests>
187 <help>
188 <![CDATA[
189
190 @MOTHUR_OVERVIEW@
191
192 **Command Documenation**
193
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
195
196 .. _tree.shared: http://www.mothur.org/wiki/Tree.shared
197
198 ]]>
199 </help>
200 <expand macro="citations"/>
201 </tool>