Mercurial > repos > iuc > mothur_unifrac_weighted

comparison unifrac.weighted.xml @ 3:30a8e74d6c80 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 22:20:06 -0400
parents c7e0bc7e19e9
children 136cb4f4b996
comparison
equal deleted inserted replaced
2:d546e649359c 3:30a8e74d6c80
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 "$tree" tree.dat && 13 ln -s '$tree' tree.dat &&
14 ln -s "$group" group.dat && 14 ln -s '$group' group.dat &&
15 ln -s "$name" name.dat && 15 ln -s '$name' name.dat &&
16 ln -s "$count" count.dat && 16 ln -s '$count' count.dat &&
17 17
18 echo 'unifrac.weighted( 18 echo 'unifrac.weighted(
19 tree=tree.dat, 19 tree=tree.dat,
20 #if $group: 20 #if $group:
21 group=group.dat, 21 group=group.dat,
22 #if $groups: 22 #if $groups:
23 groups=${ str($groups).replace(",","-") }, 23 groups=${ str($groups).replace(",","-") },
24 #end if
25 #end if
26 #if $name:
27 name=name.dat,
28 #end if
29 iters=$iters,
30 #if $subsampling.use == "yes":
31 #if $subsampling.subsample:
32 subsample=$subsampling.subsample,
33 #else
34 subsample=T,
35 #end if
36 consensus=$subsampling.consensus,
37 #else
38 random=$random,
39 #end if
40 #if $distance:
41 distance=$distance,
42 #end if
43 #if $count:
44 count=count.dat,
45 #end if
46 root=$root,
47 processors='\${GALAXY_SLOTS:-1}'
48 )'
49 | sed 's/ //g' ## mothur trips over whitespace
50 | mothur
51 | tee mothur.out.log
52 ## rename some datasets
53 #if $subsampling.use == "yes":
54 && mv tree.*.ave.dist tree.ave
55 && mv tree.*.std.dist tree.std
56 #end if 24 #end if
25 #end if
26 #if $name:
27 name=name.dat,
28 #end if
29 iters=$iters,
30 #if $subsampling.use == "yes":
31 #if $subsampling.subsample:
32 subsample=$subsampling.subsample,
33 #else
34 subsample=T,
35 #end if
36 consensus=$subsampling.consensus,
37 #else
38 random=$random,
39 #end if
40 #if $distance:
41 distance=$distance,
42 #end if
43 #if $count:
44 count=count.dat,
45 #end if
46 root=$root,
47 processors='\${GALAXY_SLOTS:-1}'
48 )'
49 | sed 's/ //g' ## mothur trips over whitespace
50 | mothur
51 | tee mothur.out.log
52
53 ## rename some datasets
54 #if $subsampling.use == "yes":
55 && mv tree.*.ave.dist tree.ave
56 && mv tree.*.std.dist tree.std
57 #end if
57 ]]></command> 58 ]]></command>
58 <inputs> 59 <inputs>
59 <param name="tree" type="data" format="mothur.tre" label="tree - Tree"/> 60 <param name="tree" type="data" format="mothur.tre" label="tree - Tree"/>
60 <param name="group" type="data" format="mothur.groups" label="group - Group file for the tree"/> 61 <param name="group" type="data" format="mothur.groups" label="group - Group file for the tree"/>
61 <param name="groups" type="select" optional="true" multiple="true" label="groups - Select groups for pairwise comparisons" help="You must select at least 2 groups"> 62 <param name="groups" type="select" optional="true" multiple="true" label="groups - Select groups for pairwise comparisons" help="You must select at least 2 groups">
82 <option value="square">Phylip Square Matrix</option> 83 <option value="square">Phylip Square Matrix</option>
83 <option value="column">Pairwise Distance Matrix</option> 84 <option value="column">Pairwise Distance Matrix</option>
84 </param> 85 </param>
85 <param name="root" type="boolean" truevalue="true" falsevalue="false" checked="false" label="root - the entire root in your calculations"/> 86 <param name="root" type="boolean" truevalue="true" falsevalue="false" checked="false" label="root - the entire root in your calculations"/>
86 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> 87 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
88 <expand macro="param-savelog"/>
87 </inputs> 89 </inputs>
88 <outputs> 90 <outputs>
89 <expand macro="logfile-output"/> 91 <expand macro="logfile-output"/>
90 <data name="summary" format="tabular" from_work_dir="tree*wsummary" label="${tool.name} on ${on_string}: summary"/> 92 <data name="summary" format="tabular" from_work_dir="tree*wsummary" label="${tool.name} on ${on_string}: summary"/>
91 <data name="dist" format="mothur.lower.dist" from_work_dir="tree.dat*.dist " label="${tool.name} on ${on_string}: dist"> 93 <data name="dist" format="mothur.lower.dist" from_work_dir="tree.dat*.dist " label="${tool.name} on ${on_string}: dist">
123 <param name="tree" value="abrecovery.tre" ftype="mothur.tre"/> 125 <param name="tree" value="abrecovery.tre" ftype="mothur.tre"/>
124 <param name="group" value="abrecovery.groups" ftype="mothur.groups"/> 126 <param name="group" value="abrecovery.groups" ftype="mothur.groups"/>
125 <param name="groups" value="A,B,C"/> 127 <param name="groups" value="A,B,C"/>
126 <output name="summary" md5="f723493c1b909f5dbe5688d36be9fe73" ftype="tabular"/> 128 <output name="summary" md5="f723493c1b909f5dbe5688d36be9fe73" ftype="tabular"/>
127 <output name="dist" md5="3660f333ac1326c8df213d1d3af1f865" ftype="mothur.lower.dist"/> 129 <output name="dist" md5="3660f333ac1326c8df213d1d3af1f865" ftype="mothur.lower.dist"/>
130 <param name="savelog" value="true"/>
128 <expand macro="logfile-test"/> 131 <expand macro="logfile-test"/>
129 </test> 132 </test>
130 <test><!-- test with random and no subsampling --> 133 <test><!-- test with random and no subsampling -->
131 <param name="tree" value="abrecovery.tre" ftype="mothur.tre"/> 134 <param name="tree" value="abrecovery.tre" ftype="mothur.tre"/>
132 <param name="group" value="abrecovery.groups" ftype="mothur.groups"/> 135 <param name="group" value="abrecovery.groups" ftype="mothur.groups"/>
139 <has_text text="A-CRandFreq"/> 142 <has_text text="A-CRandFreq"/>
140 <has_text text="B-CRandCumul"/> 143 <has_text text="B-CRandCumul"/>
141 </assert_contents> 144 </assert_contents>
142 </output> 145 </output>
143 <output name="dist" md5="3660f333ac1326c8df213d1d3af1f865" ftype="mothur.lower.dist"/> 146 <output name="dist" md5="3660f333ac1326c8df213d1d3af1f865" ftype="mothur.lower.dist"/>
147 <param name="savelog" value="true"/>
144 <expand macro="logfile-test"/> 148 <expand macro="logfile-test"/>
145 </test> 149 </test>
146 <test><!-- test with group file and group select --> 150 <test><!-- test with group file and group select -->
147 <param name="tree" value="abrecovery.tre" ftype="mothur.tre"/> 151 <param name="tree" value="abrecovery.tre" ftype="mothur.tre"/>
148 <param name="group" value="abrecovery.groups" ftype="mothur.groups"/> 152 <param name="group" value="abrecovery.groups" ftype="mothur.groups"/>
149 <param name="groups" value="A,B"/> 153 <param name="groups" value="A,B"/>
150 <param name="distance" value="square"/> 154 <param name="distance" value="square"/>
151 <output name="summary" md5="c253d4a3225804ad24b6c2e3a1095040" ftype="tabular"/> 155 <output name="summary" md5="c253d4a3225804ad24b6c2e3a1095040" ftype="tabular"/>
152 <output name="dist" md5="7df2d4a2e69b9c1259d39fe59165734f" ftype="mothur.square.dist"/> 156 <output name="dist" md5="7df2d4a2e69b9c1259d39fe59165734f" ftype="mothur.square.dist"/>
157 <param name="savelog" value="true"/>
153 <expand macro="logfile-test"/> 158 <expand macro="logfile-test"/>
154 </test> 159 </test>
155 <test><!-- test with subsample and consensus --> 160 <test><!-- test with subsample and consensus -->
156 <param name="tree" value="abrecovery.tre" ftype="mothur.tre"/> 161 <param name="tree" value="abrecovery.tre" ftype="mothur.tre"/>
157 <param name="group" value="abrecovery.groups" ftype="mothur.groups"/> 162 <param name="group" value="abrecovery.groups" ftype="mothur.groups"/>
188 <has_text text="A"/> 193 <has_text text="A"/>
189 <has_text text="B"/> 194 <has_text text="B"/>
190 <has_text text="C"/> 195 <has_text text="C"/>
191 </assert_contents> 196 </assert_contents>
192 </output> 197 </output>
198 <param name="savelog" value="true"/>
193 <expand macro="logfile-test"/> 199 <expand macro="logfile-test"/>
194 </test> 200 </test>
195 </tests> 201 </tests>
196 <help> 202 <help><![CDATA[
197 <![CDATA[
198 203
199 @MOTHUR_OVERVIEW@ 204 @MOTHUR_OVERVIEW@
200 205
201 **Command Documentation** 206 **Command Documentation**
202 207
203 The unifrac.weighted_ command implements the weighted UniFrac algorithm. The unifrac.unweighted command implements the unweighted version of the command. Both of these methods are available through the UniFrac website. The UniFrac methods are generic tests that describes whether two or more communities have the same structure. The significance of the test statistic can only indicate the probability that the communities have the same structure by chance. The value does not indicate a level of similarity. 208 The unifrac.weighted_ command implements the weighted UniFrac algorithm. The unifrac.unweighted command implements the unweighted version of the command. Both of these methods are available through the UniFrac website. The UniFrac methods are generic tests that describes whether two or more communities have the same structure. The significance of the test statistic can only indicate the probability that the communities have the same structure by chance. The value does not indicate a level of similarity.
204 209
205 .. _unifrac.weighted: https://www.mothur.org/wiki/Unifrac.weighted 210 .. _unifrac.weighted: https://www.mothur.org/wiki/Unifrac.weighted
206 211
207 ]]> 212 ]]></help>
208 </help>
209 <expand macro="citations"/> 213 <expand macro="citations"/>
210 </tool> 214 </tool>