Mercurial > repos > iuc > mothur_tree_shared

comparison tree.shared.xml @ 2:506ad7182cfb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:19:37 -0400
parents ffeb8cd81f04
children 8bca555fbcaf
comparison
equal deleted inserted replaced
1:06c8f1be0f31 2:506ad7182cfb
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$input.dist" input_dist.dat && 13 ln -s '$input.dist' input_dist.dat &&
14 #if not $input.source == "shared": 14 #if not $input.source == "shared":
15 ln -s "$input.name" input_name.dat && 15 ln -s '$input.name' input_name.dat &&
16 #end if
17
18 echo 'tree.shared(
19 #if $input.source == "shared":
20 shared=input_dist.dat,
21 #if $input.groups:
22 groups=${ str($input.groups).replace(",","-") },
16 #end if 23 #end if
17 24 #if $input.label:
18 echo 'tree.shared( 25 label=${ str($input.label).replace(",","-") },
19 #if $input.source == "shared": 26 #end if
20 shared=input_dist.dat, 27 #if $input.subsampling.use == "yes":
21 #if $input.groups: 28 #if $input.subsampling.subsample:
22 groups=${ str($input.groups).replace(",","-") }, 29 subsample=$input.subsampling.subsample,
23 #end if
24 #if $input.label:
25 label=${ str($input.label).replace(",","-") },
26 #end if
27 #if $input.subsampling.use == "yes":
28 #if $input.subsampling.subsample:
29 subsample=$input.subsampling.subsample,
30 #else
31 subsample=T,
32 #end if
33 #if $input.subsampling.iters:
34 iters="$input.subsampling.iters,
35 #end if
36 #end if
37 #elif $input.source == "column":
38 column=input_dist.dat,
39 name=input_name.dat,
40 #elif $input.source == "phylip":
41 phylip=input_dist.dat,
42 #if $input.name:
43 name=input_name.dat,
44 #end if
45 #else 30 #else
46 count=input_name.dat, 31 subsample=T,
47 #end if 32 #end if
48 #if $calc: 33 #if $input.subsampling.iters:
49 calc=${ str($calc).replace(",","-") }, 34 iters="$input.subsampling.iters,
50 #end if 35 #end if
51 processors='\${GALAXY_SLOTS:-8}' 36 #end if
52 )' 37 #elif $input.source == "column":
53 | sed 's/ //g' ## mothur trips over whitespace 38 column=input_dist.dat,
54 | mothur 39 name=input_name.dat,
55 | tee mothur.out.log 40 #elif $input.source == "phylip":
41 phylip=input_dist.dat,
42 #if $input.name:
43 name=input_name.dat,
44 #end if
45 #else
46 count=input_name.dat,
47 #end if
48 #if $calc:
49 calc=${ str($calc).replace(",","-") },
50 #end if
51 processors='\${GALAXY_SLOTS:-8}'
52 )'
53 | sed 's/ //g' ## mothur trips over whitespace
54 | mothur
55 | tee mothur.out.log
56 ]]></command> 56 ]]></command>
57 <inputs> 57 <inputs>
58 <conditional name="input"> 58 <conditional name="input">
59 <param name="source" type="select" label="Select input format"> 59 <param name="source" type="select" label="Select input format">
60 <option value="shared">OTU Shared</option> 60 <option value="shared">OTU Shared</option>
103 <expand macro="calc-common"/> 103 <expand macro="calc-common"/>
104 <!-- set default option(s) --> 104 <!-- set default option(s) -->
105 <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option> 105 <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
106 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option> 106 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
107 </param> 107 </param>
108 <expand macro="param-savelog"/>
108 </inputs> 109 </inputs>
109 <outputs> 110 <outputs>
110 <expand macro="logfile-output"/> 111 <expand macro="logfile-output"/>
111 <data name="tre" format="mothur.tre" from_work_dir="input_dist*.tre" label="${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> 160 <help><![CDATA[
156 <![CDATA[
157 161
158 @MOTHUR_OVERVIEW@ 162 @MOTHUR_OVERVIEW@
159 163
160 **Command Documentation** 164 **Command Documentation**
161 165
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 166 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
163 167
164 .. _tree.shared: https://www.mothur.org/wiki/Tree.shared 168 .. _tree.shared: https://www.mothur.org/wiki/Tree.shared
165 169
166 ]]> 170 ]]></help>
167 </help>
168 <expand macro="citations"/> 171 <expand macro="citations"/>
169 </tool> 172 </tool>