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Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
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1 <tool id="beta_diversity" name="beta_diversity" version="1.2.0">
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_tmpdir='$__new_file_path__'
9 #set datasets = []
10 #if $binary_chisq.__str__ != "None":
11 #set datasets = $datasets + ["'binary_chisq_.*$:'" + $binary_chisq.__str__]
12 #end if
13 #if $binary_chord.__str__ != "None":
14 #set datasets = $datasets + ["'binary_chord_.*$:'" + $binary_chord.__str__]
15 #end if
16 #if $binary_euclidean.__str__ != "None":
17 #set datasets = $datasets + ["'binary_euclidean_.*$:'" + $binary_euclidean.__str__]
18 #end if
19 #if $binary_hamming.__str__ != "None":
20 #set datasets = $datasets + ["'binary_hamming_.*$:'" + $binary_hamming.__str__]
21 #end if
22 #if $binary_jaccard.__str__ != "None":
23 #set datasets = $datasets + ["'binary_jaccard_.*$:'" + $binary_jaccard.__str__]
24 #end if
25 #if $binary_lennon.__str__ != "None":
26 #set datasets = $datasets + ["'binary_lennon_.*$:'" + $binary_lennon.__str__]
27 #end if
28 #if $binary_ochiai.__str__ != "None":
29 #set datasets = $datasets + ["'binary_ochiai_.*$:'" + $binary_ochiai.__str__]
30 #end if
31 #if $binary_pearson.__str__ != "None":
32 #set datasets = $datasets + ["'binary_pearson_.*$:'" + $binary_pearson.__str__]
33 #end if
34 #if $binary_sorensen_dice.__str__ != "None":
35 #set datasets = $datasets + ["'binary_sorensen_dice_.*$:'" + $binary_sorensen_dice.__str__]
36 #end if
37 #if $bray_curtis.__str__ != "None":
38 #set datasets = $datasets + ["'bray_curtis_.*$:'" + $bray_curtis.__str__]
39 #end if
40 #if $canberra.__str__ != "None":
41 #set datasets = $datasets + ["'canberra_.*$:'" + $canberra.__str__]
42 #end if
43 #if $chisq.__str__ != "None":
44 #set datasets = $datasets + ["'chisq_.*$:'" + $chisq.__str__]
45 #end if
46 #if $chord.__str__ != "None":
47 #set datasets = $datasets + ["'chord_.*$:'" + $chord.__str__]
48 #end if
49 #if $euclidean.__str__ != "None":
50 #set datasets = $datasets + ["'euclidean_.*$:'" + $euclidean.__str__]
51 #end if
52 #if $gower.__str__ != "None":
53 #set datasets = $datasets + ["'gower_.*$:'" + $gower.__str__]
54 #end if
55 #if $hellinger.__str__ != "None":
56 #set datasets = $datasets + ["'hellinger_.*$:'" + $hellinger.__str__]
57 #end if
58 #if $kulczynski.__str__ != "None":
59 #set datasets = $datasets + ["'kulczynski_.*$:'" + $kulczynski.__str__]
60 #end if
61 #if $manhattan.__str__ != "None":
62 #set datasets = $datasets + ["'manhattan_.*$:'" + $manhattan.__str__]
63 #end if
64 #if $morisita_horn.__str__ != "None":
65 #set datasets = $datasets + ["'morisita_horn_.*$:'" + $morisita_horn.__str__]
66 #end if
67 #if $pearson.__str__ != "None":
68 #set datasets = $datasets + ["'pearson_.*$:'" + $pearson.__str__]
69 #end if
70 #if $soergel.__str__ != "None":
71 #set datasets = $datasets + ["'soergel_.*$:'" + $soergel.__str__]
72 #end if
73 #if $spearman_approx.__str__ != "None":
74 #set datasets = $datasets + ["'spearman_approx_.*$:'" + $spearman_approx.__str__]
75 #end if
76 #if $specprof.__str__ != "None":
77 #set datasets = $datasets + ["'specprof_.*$:'" + $specprof.__str__]
78 #end if
79 #if $unifrac.__str__ != "None":
80 #set datasets = $datasets + ["'unifrac_.*$:'" + $unifrac.__str__]
81 #end if
82 #if $unifrac_g.__str__ != "None":
83 #set datasets = $datasets + ["'unifrac_g_.*$:'" + $unifrac_g.__str__]
84 #end if
85 #if $unifrac_g_full_tree.__str__ != "None":
86 #set datasets = $datasets + ["'unifrac_g_full_tree_.*$:'" + $unifrac_g_full_tree.__str__]
87 #end if
88 #if $unweighted_unifrac.__str__ != "None":
89 #set datasets = $datasets + ["'unweighted_unifrac_.*$:'" + $unweighted_unifrac.__str__]
90 #end if
91 #if $unweighted_unifrac_full_tree.__str__ != "None":
92 #set datasets = $datasets + ["'unweighted_unifrac_full_tree_.*$:'" + $unweighted_unifrac_full_tree.__str__]
93 #end if
94 #if $weighted_normalized_unifrac.__str__ != "None":
95 #set datasets = $datasets + ["'weighted_normalized_unifrac_.*$:'" + $weighted_normalized_unifrac.__str__]
96 #end if
97 #if $weighted_unifrac.__str__ != "None":
98 #set datasets = $datasets + ["'weighted_unifrac_.*$:'" + $weighted_unifrac.__str__]
99 #end if
100 --galaxy_datasets=#echo ','.join($datasets)
101 beta_diversity.py
102 --input_path=$input_path
103 #if $rows.__str__ != '':
104 --rows=$rows
105 #end if
106 --output_dir=$__new_file_path__
107 --metrics=$metrics
108 #if $tree_path.__str__ != "None" and len($tree_path.__str__) > 0:
109 --tree_path=$tree_path
110 #end if
111 $full_tree
112 </command>
113 <inputs>
114 <param name="input_path" type="data" format="qiimeotutable" label="input_path"
115 help="input path: otu table"/>
116 <param name="rows" type="text" label="rows"
117 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]"/>
118 <param name="metrics" type="select" multiple="true" label="metrics" help="metrics to use">
119 <option value="abund_jaccard">abund_jaccard</option>
120 <option value="binary_chisq">binary_chisq</option>
121 <option value="binary_chord">binary_chord</option>
122 <option value="binary_euclidean">binary_euclidean</option>
123 <option value="binary_hamming">binary_hamming</option>
124 <option value="binary_jaccard">binary_jaccard</option>
125 <option value="binary_lennon">binary_lennon</option>
126 <option value="binary_ochiai">binary_ochiai</option>
127 <option value="binary_otu_gain">binary_otu_gain</option>
128 <option value="binary_pearson">binary_pearson</option>
129 <option value="binary_sorensen_dice">binary_sorensen_dice</option>
130 <option value="bray_curtis">bray_curtis</option>
131 <option value="canberra">canberra</option>
132 <option value="chisq">chisq</option>
133 <option value="chord">chord</option>
134 <option value="euclidean">euclidean</option>
135 <option value="gower">gower</option>
136 <option value="hellinger">hellinger</option>
137 <option value="kulczynski">kulczynski</option>
138 <option value="manhattan">manhattan</option>
139 <option value="morisita_horn">morisita_horn</option>
140 <option value="pearson">pearson</option>
141 <option value="soergel">soergel</option>
142 <option value="spearman_approx">spearman_approx</option>
143 <option value="specprof">specprof</option>
144 <option value="unifrac">unifrac</option>
145 <option value="unifrac_g">unifrac_g</option>
146 <option value="unifrac_g_full_tree">unifrac_g_full_tree</option>
147 <option value="unweighted_unifrac">unweighted_unifrac</option>
148 <option value="unweighted_unifrac_full_tree">unweighted_unifrac_full_tree</option>
149 <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option>
150 <option value="weighted_unifrac">weighted_unifrac</option>
151 </param>
152 <param name="tree_path" type="text" label="tree_path"
153 help="path to newick tree file, required for phylogenetic metrics [default: %default]"/>
154 <param name="full_tree" type="boolean" truevalue="--full_tree" falsevalue="" checked="false" label="full_tree"
155 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"/>
156 </inputs>
157 <outputs>
158 <data format="qiimedistmat" name="binary_chisq" label="${tool.name} on ${on_string}: binary_chisq.dist">
159 <filter>'binary_chisq' in (metrics if isinstance(metrics,list) else [metrics])</filter>
160 </data>
161 <data format="qiimedistmat" name="binary_chord" label="${tool.name} on ${on_string}: binary_chord.dist">
162 <filter>'binary_chord' in (metrics if isinstance(metrics,list) else [metrics])</filter>
163 </data>
164 <data format="qiimedistmat" name="binary_euclidean" label="${tool.name} on ${on_string}: binary_euclidean.dist">
165 <filter>'binary_euclidean' in (metrics if isinstance(metrics,list) else [metrics])</filter>
166 </data>
167 <data format="qiimedistmat" name="binary_hamming" label="${tool.name} on ${on_string}: binary_hamming.dist">
168 <filter>'binary_hamming' in (metrics if isinstance(metrics,list) else [metrics])</filter>
169 </data>
170 <data format="qiimedistmat" name="binary_jaccard" label="${tool.name} on ${on_string}: binary_jaccard.dist">
171 <filter>'binary_jaccard' in (metrics if isinstance(metrics,list) else [metrics])</filter>
172 </data>
173 <data format="qiimedistmat" name="binary_lennon" label="${tool.name} on ${on_string}: binary_lennon.dist">
174 <filter>'binary_lennon' in (metrics if isinstance(metrics,list) else [metrics])</filter>
175 </data>
176 <data format="qiimedistmat" name="binary_ochiai" label="${tool.name} on ${on_string}: binary_ochiai.dist">
177 <filter>'binary_ochiai' in (metrics if isinstance(metrics,list) else [metrics])</filter>
178 </data>
179 <data format="qiimedistmat" name="binary_pearson" label="${tool.name} on ${on_string}: binary_pearson.dist">
180 <filter>'binary_pearson' in (metrics if isinstance(metrics,list) else [metrics])</filter>
181 </data>
182 <data format="qiimedistmat" name="binary_sorensen_dice" label="${tool.name} on ${on_string}: binary_sorensen_dice.dist">
183 <filter>'binary_sorensen_dice' in (metrics if isinstance(metrics,list) else [metrics])</filter>
184 </data>
185 <data format="qiimedistmat" name="bray_curtis" label="${tool.name} on ${on_string}: bray_curtis.dist">
186 <filter>'bray_curtis' in (metrics if isinstance(metrics,list) else [metrics])</filter>
187 </data>
188 <data format="qiimedistmat" name="canberra" label="${tool.name} on ${on_string}: canberra.dist">
189 <filter>'canberra' in (metrics if isinstance(metrics,list) else [metrics])</filter>
190 </data>
191 <data format="qiimedistmat" name="chisq" label="${tool.name} on ${on_string}: chisq.dist">
192 <filter>'chisq' in (metrics if isinstance(metrics,list) else [metrics])</filter>
193 </data>
194 <data format="qiimedistmat" name="chord" label="${tool.name} on ${on_string}: chord.dist">
195 <filter>'chord' in (metrics if isinstance(metrics,list) else [metrics])</filter>
196 </data>
197 <data format="qiimedistmat" name="euclidean" label="${tool.name} on ${on_string}: euclidean.dist">
198 <filter>'euclidean' in (metrics if isinstance(metrics,list) else [metrics])</filter>
199 </data>
200 <data format="qiimedistmat" name="gower" label="${tool.name} on ${on_string}: gower.dist">
201 <filter>'gower' in (metrics if isinstance(metrics,list) else [metrics])</filter>
202 </data>
203 <data format="qiimedistmat" name="hellinger" label="${tool.name} on ${on_string}: hellinger.dist">
204 <filter>'hellinger' in (metrics if isinstance(metrics,list) else [metrics])</filter>
205 </data>
206 <data format="qiimedistmat" name="kulczynski" label="${tool.name} on ${on_string}: kulczynski.dist">
207 <filter>'kulczynski' in (metrics if isinstance(metrics,list) else [metrics])</filter>
208 </data>
209 <data format="qiimedistmat" name="manhattan" label="${tool.name} on ${on_string}: manhattan.dist">
210 <filter>'manhattan' in (metrics if isinstance(metrics,list) else [metrics])</filter>
211 </data>
212 <data format="qiimedistmat" name="morisita_horn" label="${tool.name} on ${on_string}: morisita_horn.dist">
213 <filter>'morisita_horn' in (metrics if isinstance(metrics,list) else [metrics])</filter>
214 </data>
215 <data format="qiimedistmat" name="pearson" label="${tool.name} on ${on_string}: pearson.dist">
216 <filter>'pearson' in (metrics if isinstance(metrics,list) else [metrics])</filter>
217 </data>
218 <data format="qiimedistmat" name="soergel" label="${tool.name} on ${on_string}: soergel.dist">
219 <filter>'soergel' in (metrics if isinstance(metrics,list) else [metrics])</filter>
220 </data>
221 <data format="qiimedistmat" name="spearman_approx" label="${tool.name} on ${on_string}: spearman_approx.dist">
222 <filter>'spearman_approx' in (metrics if isinstance(metrics,list) else [metrics])</filter>
223 </data>
224 <data format="qiimedistmat" name="specprof" label="${tool.name} on ${on_string}: specprof.dist">
225 <filter>'specprof' in (metrics if isinstance(metrics,list) else [metrics])</filter>
226 </data>
227 <data format="qiimedistmat" name="unifrac" label="${tool.name} on ${on_string}: unifrac.dist">
228 <filter>'unifrac' in (metrics if isinstance(metrics,list) else [metrics])</filter>
229 </data>
230 <data format="qiimedistmat" name="unifrac_g" label="${tool.name} on ${on_string}: unifrac_g.dist">
231 <filter>'unifrac_g' in (metrics if isinstance(metrics,list) else [metrics])</filter>
232 </data>
233 <data format="qiimedistmat" name="unifrac_g_full_tree" label="${tool.name} on ${on_string}: unifrac_g_full_tree.dist">
234 <filter>'unifrac_g_full_tree' in (metrics if isinstance(metrics,list) else [metrics])</filter>
235 </data>
236 <data format="qiimedistmat" name="unweighted_unifrac" label="${tool.name} on ${on_string}: unweighted_unifrac.dist">
237 <filter>'unweighted_unifrac' in (metrics if isinstance(metrics,list) else [metrics])</filter>
238 </data>
239 <data format="qiimedistmat" name="unweighted_unifrac_full_tree" label="${tool.name} on ${on_string}: unweighted_unifrac_full_tree.dist">
240 <filter>'unweighted_unifrac_full_tree' in (metrics if isinstance(metrics,list) else [metrics])</filter>
241 </data>
242 <data format="qiimedistmat" name="weighted_normalized_unifrac" label="${tool.name} on ${on_string}: weighted_normalized_unifrac.dist">
243 <filter>'weighted_normalized_unifrac' in (metrics if isinstance(metrics,list) else [metrics])</filter>
244 </data>
245 <data format="qiimedistmat" name="weighted_unifrac" label="${tool.name} on ${on_string}: weighted_unifrac.dist">
246 <filter>'weighted_unifrac' in (metrics if isinstance(metrics,list) else [metrics])</filter>
247 </data>
248 </outputs>
249 <tests>
250 </tests>
251 <help>
252
253 </help>
254 </tool>
255