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author azuzolo
date Wed, 06 Jun 2012 16:40:30 -0400
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1 <tool id="beta_diversity" name="beta_diversity" version="2.0.0">
2 <description>Calculate beta diversity (pairwise sample dissimilarity) on one or many otu tables</description>
3 <requirements>
4 <requirement type="binary">beta_diversity.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 --galaxy_outputdir=$__new_file_path__
9 #set datasets = []
10 #set $path = ""
11 #if $binary_chisq.__str__ != "None":
12 #set datasets = $datasets + ["'binary_chisq_.*$:'" + $binary_chisq.__str__]
13 #if path == "":
14 #set $path=$binary_chisq.extra_files_path
15 #end if
16 #end if
17 #if $binary_chord.__str__ != "None":
18 #set datasets = $datasets + ["'binary_chord_.*$:'" + $binary_chord.__str__]
19 #if path == "":
20 #set $path=$binary_chord.extra_files_path
21 #end if
22 #end if
23 #if $binary_euclidean.__str__ != "None":
24 #set datasets = $datasets + ["'binary_euclidean_.*$:'" + $binary_euclidean.__str__]
25 #if path == "":
26 #set $path=$binary_euclidean.extra_files_path
27 #end if
28 #end if
29 #if $binary_hamming.__str__ != "None":
30 #set datasets = $datasets + ["'binary_hamming_.*$:'" + $binary_hamming.__str__]
31 #if path == "":
32 #set $path=$binary_hamming.extra_files_path
33 #end if
34 #end if
35 #if $binary_jaccard.__str__ != "None":
36 #set datasets = $datasets + ["'binary_jaccard_.*$:'" + $binary_jaccard.__str__]
37 #if path == "":
38 #set $path=$binary_jaccard.extra_files_path
39 #end if
40 #end if
41 #if $binary_lennon.__str__ != "None":
42 #set datasets = $datasets + ["'binary_lennon_.*$:'" + $binary_lennon.__str__]
43 #if path == "":
44 #set $path=$binary_lennon.extra_files_path
45 #end if
46 #end if
47 #if $binary_ochiai.__str__ != "None":
48 #set datasets = $datasets + ["'binary_ochiai_.*$:'" + $binary_ochiai.__str__]
49 #if path == "":
50 #set $path=$binary_ochiai.extra_files_path
51 #end if
52 #end if
53 #if $binary_pearson.__str__ != "None":
54 #set datasets = $datasets + ["'binary_pearson_.*$:'" + $binary_pearson.__str__]
55 #if path == "":
56 #set $path=$binary_pearson.extra_files_path
57 #end if
58 #end if
59 #if $binary_sorensen_dice.__str__ != "None":
60 #set datasets = $datasets + ["'binary_sorensen_dice_.*$:'" + $binary_sorensen_dice.__str__]
61 #if path == "":
62 #set $path=$binary_sorensen.extra_files_path
63 #end if
64 #end if
65 #if $bray_curtis.__str__ != "None":
66 #set datasets = $datasets + ["'bray_curtis_.*$:'" + $bray_curtis.__str__]
67 #if path == "":
68 #set $path=$bray_curtis.extra_files_path
69 #end if
70 #end if
71 #if $canberra.__str__ != "None":
72 #set datasets = $datasets + ["'canberra_.*$:'" + $canberra.__str__]
73 #if path == "":
74 #set $path=$canberra.extra_files_path
75 #end if
76 #end if
77 #if $chisq.__str__ != "None":
78 #set datasets = $datasets + ["'chisq_.*$:'" + $chisq.__str__]
79 #if path == "":
80 #set $path=$binary_euclidean.extra_files_path
81 #end if
82 #end if
83 #if $chord.__str__ != "None":
84 #set datasets = $datasets + ["'chord_.*$:'" + $chord.__str__]
85 #if path == "":
86 #set $path=$chord.extra_files_path
87 #end if
88 #end if
89 #if $euclidean.__str__ != "None":
90 #set datasets = $datasets + ["'euclidean_.*$:'" + $euclidean.__str__]
91 #if path == "":
92 #set $path=$euclidean.extra_files_path
93 #end if
94 #end if
95 #if $gower.__str__ != "None":
96 #set datasets = $datasets + ["'gower_.*$:'" + $gower.__str__]
97 #if path == "":
98 #set $path=$gower.extra_files_path
99 #end if
100 #end if
101 #if $hellinger.__str__ != "None":
102 #set datasets = $datasets + ["'hellinger_.*$:'" + $hellinger.__str__]
103 #if path == "":
104 #set $path=$hellinger.extra_files_path
105 #end if
106 #end if
107 #if $kulczynski.__str__ != "None":
108 #set datasets = $datasets + ["'kulczynski_.*$:'" + $kulczynski.__str__]
109 #if path == "":
110 #set $path=$kulczynski.extra_files_path
111 #end if
112 #end if
113 #if $manhattan.__str__ != "None":
114 #set datasets = $datasets + ["'manhattan_.*$:'" + $manhattan.__str__]
115 #if path == "":
116 #set $path=$manhattan.extra_files_path
117 #end if
118 #end if
119 #if $morisita_horn.__str__ != "None":
120 #set datasets = $datasets + ["'morisita_horn_.*$:'" + $morisita_horn.__str__]
121 #if path == "":
122 #set $path=$morisita_horn.extra_files_path
123 #end if
124 #end if
125 #if $pearson.__str__ != "None":
126 #set datasets = $datasets + ["'pearson_.*$:'" + $pearson.__str__]
127 #if path == "":
128 #set $path=$pearson.extra_files_path
129 #end if
130 #end if
131 #if $soergel.__str__ != "None":
132 #set datasets = $datasets + ["'soergel_.*$:'" + $soergel.__str__]
133 #if path == "":
134 #set $path=$soergel.extra_files_path
135 #end if
136 #end if
137 #if $spearman_approx.__str__ != "None":
138 #set datasets = $datasets + ["'spearman_approx_.*$:'" + $spearman_approx.__str__]
139 #if path == "":
140 #set $path=$spearman_approx.extra_files_path
141 #end if
142 #end if
143 #if $specprof.__str__ != "None":
144 #set datasets = $datasets + ["'specprof_.*$:'" + $specprof.__str__]
145 #if path == "":
146 #set $path=$specprof.extra_files_path
147 #end if
148 #end if
149 #if $unifrac.__str__ != "None":
150 #set datasets = $datasets + ["'unifrac_.*$:'" + $unifrac.__str__]
151 #if path == "":
152 #set $path=$unifrac.extra_files_path
153 #end if
154 #end if
155 #if $unifrac_g.__str__ != "None":
156 #set datasets = $datasets + ["'unifrac_g_.*$:'" + $unifrac_g.__str__]
157 #if path == "":
158 #set $path=$unifrac_g.extra_files_path
159 #end if
160 #end if
161 #if $unifrac_g_full_tree.__str__ != "None":
162 #set datasets = $datasets + ["'unifrac_g_full_tree_.*$:'" + $unifrac_g_full_tree.__str__]
163 #if path == "":
164 #set $path=$unifrac_g_full_tree.extra_files_path
165 #end if
166 #end if
167 #if $unweighted_unifrac.__str__ != "None":
168 #set datasets = $datasets + ["'unweighted_unifrac_.*$:'" + $unweighted_unifrac.__str__]
169 #if path == "":
170 #set $path=$unweighted_unifrac.extra_files_path
171 #end if
172 #end if
173 #if $unweighted_unifrac_full_tree.__str__ != "None":
174 #set datasets = $datasets + ["'unweighted_unifrac_full_tree_.*$:'" + $unweighted_unifrac_full_tree.__str__]
175 #if path == "":
176 #set $path=$unweighted_unifrac_full_tree.extra_files_path
177 #end if
178 #end if
179 #if $weighted_normalized_unifrac.__str__ != "None":
180 #set datasets = $datasets + ["'weighted_normalized_unifrac_.*$:'" + $weighted_normalized_unifrac.__str__]
181 #if path == "":
182 #set $path=$weighted_normalized_unifrac.extra_files_path
183 #end if
184 #end if
185 #if $weighted_unifrac.__str__ != "None":
186 #set datasets = $datasets + ["'weighted_unifrac_.*$:'" + $weighted_unifrac.__str__]
187 #if path == "":
188 #set $path=$weighted_unifrac.extra_files_path
189 #end if
190 #end if
191 --galaxy_datasets=#echo ','.join($datasets)
192 --galaxy_new_files_path='$path'
193 beta_diversity.py
194 --input_path=$input_path
195 #if $rows.__str__ != '':
196 --rows=$rows
197 #end if
198 --output_dir=$__new_file_path__
199 --metrics=$metrics
200 #if $tree_path.__str__ != "None" and len($tree_path.__str__) > 0:
201 --tree_path=$tree_path
202 #end if
203 $full_tree
204 </command>
205 <inputs>
206 <param name="input_path" type="data" format="qiimeotutable" label="input_path"
207 help="input path: otu table (e.g., output from make_otu_table or single_rarefaction)"/>
208 <param name="rows" type="text" label="rows"
209 help="compute only these rows of the distance matrix. pass a list of sample names, e.g. 's1,s3' [by default, + the full n x n matrix is generated]"/>
210 <param name="metrics" type="select" multiple="true" label="metrics" help="metrics to use">
211 <option value="abund_jaccard">abund_jaccard</option>
212 <option value="binary_chisq">binary_chisq</option>
213 <option value="binary_chord">binary_chord</option>
214 <option value="binary_euclidean">binary_euclidean</option>
215 <option value="binary_hamming">binary_hamming</option>
216 <option value="binary_jaccard">binary_jaccard</option>
217 <option value="binary_lennon">binary_lennon</option>
218 <option value="binary_ochiai">binary_ochiai</option>
219 <option value="binary_otu_gain">binary_otu_gain</option>
220 <option value="binary_pearson">binary_pearson</option>
221 <option value="binary_sorensen_dice">binary_sorensen_dice</option>
222 <option value="bray_curtis">bray_curtis</option>
223 <option value="canberra">canberra</option>
224 <option value="chisq">chisq</option>
225 <option value="chord">chord</option>
226 <option value="euclidean">euclidean</option>
227 <option value="gower">gower</option>
228 <option value="hellinger">hellinger</option>
229 <option value="kulczynski">kulczynski</option>
230 <option value="manhattan">manhattan</option>
231 <option value="morisita_horn">morisita_horn</option>
232 <option value="pearson">pearson</option>
233 <option value="soergel">soergel</option>
234 <option value="spearman_approx">spearman_approx</option>
235 <option value="specprof">specprof</option>
236 <option value="unifrac">unifrac</option>
237 <option value="unifrac_g">unifrac_g</option>
238 <option value="unifrac_g_full_tree">unifrac_g_full_tree</option>
239 <option value="unweighted_unifrac">unweighted_unifrac</option>
240 <option value="unweighted_unifrac_full_tree">unweighted_unifrac_full_tree</option>
241 <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option>
242 <option value="weighted_unifrac">weighted_unifrac</option>
243 </param>
244 <param name="tree_path" type="data" optional="true" label="tree_path"
245 help="path to newick tree file, required for phylogenetic metrics [default: None]"/>
246 <param name="full_tree" type="boolean" truevalue="--full_tree" falsevalue="" checked="false" label="full_tree"
247 help="by default, we first compute the intersection of the tree with the otus present in the otu table. pass -f if you already have a minimal tree, and this script will run faster"/>
248 </inputs>
249 <outputs>
250 <data format="qiimedistmat" name="binary_chisq" label="${tool.name} on ${on_string}: binary_chisq.dist">
251 <filter>'binary_chisq' in (metrics if isinstance(metrics,list) else [metrics])</filter>
252 </data>
253 <data format="qiimedistmat" name="binary_chord" label="${tool.name} on ${on_string}: binary_chord.dist">
254 <filter>'binary_chord' in (metrics if isinstance(metrics,list) else [metrics])</filter>
255 </data>
256 <data format="qiimedistmat" name="binary_euclidean" label="${tool.name} on ${on_string}: binary_euclidean.dist">
257 <filter>'binary_euclidean' in (metrics if isinstance(metrics,list) else [metrics])</filter>
258 </data>
259 <data format="qiimedistmat" name="binary_hamming" label="${tool.name} on ${on_string}: binary_hamming.dist">
260 <filter>'binary_hamming' in (metrics if isinstance(metrics,list) else [metrics])</filter>
261 </data>
262 <data format="qiimedistmat" name="binary_jaccard" label="${tool.name} on ${on_string}: binary_jaccard.dist">
263 <filter>'binary_jaccard' in (metrics if isinstance(metrics,list) else [metrics])</filter>
264 </data>
265 <data format="qiimedistmat" name="binary_lennon" label="${tool.name} on ${on_string}: binary_lennon.dist">
266 <filter>'binary_lennon' in (metrics if isinstance(metrics,list) else [metrics])</filter>
267 </data>
268 <data format="qiimedistmat" name="binary_ochiai" label="${tool.name} on ${on_string}: binary_ochiai.dist">
269 <filter>'binary_ochiai' in (metrics if isinstance(metrics,list) else [metrics])</filter>
270 </data>
271 <data format="qiimedistmat" name="binary_pearson" label="${tool.name} on ${on_string}: binary_pearson.dist">
272 <filter>'binary_pearson' in (metrics if isinstance(metrics,list) else [metrics])</filter>
273 </data>
274 <data format="qiimedistmat" name="binary_sorensen_dice" label="${tool.name} on ${on_string}: binary_sorensen_dice.dist">
275 <filter>'binary_sorensen_dice' in (metrics if isinstance(metrics,list) else [metrics])</filter>
276 </data>
277 <data format="qiimedistmat" name="bray_curtis" label="${tool.name} on ${on_string}: bray_curtis.dist">
278 <filter>'bray_curtis' in (metrics if isinstance(metrics,list) else [metrics])</filter>
279 </data>
280 <data format="qiimedistmat" name="canberra" label="${tool.name} on ${on_string}: canberra.dist">
281 <filter>'canberra' in (metrics if isinstance(metrics,list) else [metrics])</filter>
282 </data>
283 <data format="qiimedistmat" name="chisq" label="${tool.name} on ${on_string}: chisq.dist">
284 <filter>'chisq' in (metrics if isinstance(metrics,list) else [metrics])</filter>
285 </data>
286 <data format="qiimedistmat" name="chord" label="${tool.name} on ${on_string}: chord.dist">
287 <filter>'chord' in (metrics if isinstance(metrics,list) else [metrics])</filter>
288 </data>
289 <data format="qiimedistmat" name="euclidean" label="${tool.name} on ${on_string}: euclidean.dist">
290 <filter>'euclidean' in (metrics if isinstance(metrics,list) else [metrics])</filter>
291 </data>
292 <data format="qiimedistmat" name="gower" label="${tool.name} on ${on_string}: gower.dist">
293 <filter>'gower' in (metrics if isinstance(metrics,list) else [metrics])</filter>
294 </data>
295 <data format="qiimedistmat" name="hellinger" label="${tool.name} on ${on_string}: hellinger.dist">
296 <filter>'hellinger' in (metrics if isinstance(metrics,list) else [metrics])</filter>
297 </data>
298 <data format="qiimedistmat" name="kulczynski" label="${tool.name} on ${on_string}: kulczynski.dist">
299 <filter>'kulczynski' in (metrics if isinstance(metrics,list) else [metrics])</filter>
300 </data>
301 <data format="qiimedistmat" name="manhattan" label="${tool.name} on ${on_string}: manhattan.dist">
302 <filter>'manhattan' in (metrics if isinstance(metrics,list) else [metrics])</filter>
303 </data>
304 <data format="qiimedistmat" name="morisita_horn" label="${tool.name} on ${on_string}: morisita_horn.dist">
305 <filter>'morisita_horn' in (metrics if isinstance(metrics,list) else [metrics])</filter>
306 </data>
307 <data format="qiimedistmat" name="pearson" label="${tool.name} on ${on_string}: pearson.dist">
308 <filter>'pearson' in (metrics if isinstance(metrics,list) else [metrics])</filter>
309 </data>
310 <data format="qiimedistmat" name="soergel" label="${tool.name} on ${on_string}: soergel.dist">
311 <filter>'soergel' in (metrics if isinstance(metrics,list) else [metrics])</filter>
312 </data>
313 <data format="qiimedistmat" name="spearman_approx" label="${tool.name} on ${on_string}: spearman_approx.dist">
314 <filter>'spearman_approx' in (metrics if isinstance(metrics,list) else [metrics])</filter>
315 </data>
316 <data format="qiimedistmat" name="specprof" label="${tool.name} on ${on_string}: specprof.dist">
317 <filter>'specprof' in (metrics if isinstance(metrics,list) else [metrics])</filter>
318 </data>
319 <data format="qiimedistmat" name="unifrac" label="${tool.name} on ${on_string}: unifrac.dist">
320 <filter>'unifrac' in (metrics if isinstance(metrics,list) else [metrics])</filter>
321 </data>
322 <data format="qiimedistmat" name="unifrac_g" label="${tool.name} on ${on_string}: unifrac_g.dist">
323 <filter>'unifrac_g' in (metrics if isinstance(metrics,list) else [metrics])</filter>
324 </data>
325 <data format="qiimedistmat" name="unifrac_g_full_tree" label="${tool.name} on ${on_string}: unifrac_g_full_tree.dist">
326 <filter>'unifrac_g_full_tree' in (metrics if isinstance(metrics,list) else [metrics])</filter>
327 </data>
328 <data format="qiimedistmat" name="unweighted_unifrac" label="${tool.name} on ${on_string}: unweighted_unifrac.dist">
329 <filter>'unweighted_unifrac' in (metrics if isinstance(metrics,list) else [metrics])</filter>
330 </data>
331 <data format="qiimedistmat" name="unweighted_unifrac_full_tree" label="${tool.name} on ${on_string}: unweighted_unifrac_full_tree.dist">
332 <filter>'unweighted_unifrac_full_tree' in (metrics if isinstance(metrics,list) else [metrics])</filter>
333 </data>
334 <data format="qiimedistmat" name="weighted_normalized_unifrac" label="${tool.name} on ${on_string}: weighted_normalized_unifrac.dist">
335 <filter>'weighted_normalized_unifrac' in (metrics if isinstance(metrics,list) else [metrics])</filter>
336 </data>
337 <data format="qiimedistmat" name="weighted_unifrac" label="${tool.name} on ${on_string}: weighted_unifrac.dist">
338 <filter>'weighted_unifrac' in (metrics if isinstance(metrics,list) else [metrics])</filter>
339 </data>
340 </outputs>
341 <tests>
342 </tests>
343 <help>For more information, see beta_diversity_ in the Qiime documentation.
344
345 Updated and validated 01/18/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA
346
347 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
348
349 .. _beta_diversity: http://qiime.org/scripts/beta_diversity.html</help>
350 </tool>
351