Mercurial > repos > iuc > mothur_sub_sample
comparison sub.sample.xml @ 0:be6c106b1960 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 05:55:16 -0400 |
parents | |
children | 46d13e8c60ba |
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-1:000000000000 | 0:be6c106b1960 |
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1 <tool profile="16.07" id="mothur_sub_sample" name="Sub.sample" version="@WRAPPER_VERSION@.0"> | |
2 <description>Create a sub sample</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <expand macro="stdio"/> | |
8 <expand macro="version_command"/> | |
9 <command><![CDATA[ | |
10 @SHELL_OPTIONS@ | |
11 | |
12 ## create symlinks to input datasets | |
13 ln -s "$input.otu" input_otu.dat && | |
14 ln -s "$count" count.dat && | |
15 ln -s "$taxonomy" taxonomy.dat && | |
16 #if $input.format == "fasta": | |
17 ln -s "$input.name_in" input_name_in.dat && | |
18 #end if | |
19 #if ($input.format == "fasta" or $input.format == "list") and $input.use_group.to_filter == "yes": | |
20 ln -s "$input.use_group.group_in" input_use_group_group_in.dat && | |
21 #end if | |
22 | |
23 echo 'sub.sample( | |
24 #if $input.format == "fasta": | |
25 fasta=input_otu.dat | |
26 #if $input.name_in: | |
27 ,name=input_name_in.dat | |
28 #end if | |
29 #else | |
30 #if $input.format == "list": | |
31 list=input_otu.dat | |
32 #elif $input.format == "sabund": | |
33 sabund=input_otu.dat | |
34 #elif $input.format == "rabund": | |
35 rabund=input_otu.dat | |
36 #elif $input.format == "shared": | |
37 shared=input_otu.dat | |
38 #if $input.groups: | |
39 ,groups=${ str($input.groups).replace(",","-") } | |
40 #end if | |
41 #end if | |
42 #if $input.label: | |
43 ,label=${ str($input.label).replace(",","-") } | |
44 #end if | |
45 #end if | |
46 #if $input.format == "fasta" or $input.format == "list": | |
47 #if $input.use_group.to_filter == "yes": | |
48 ,group=input_use_group_group_in.dat | |
49 #if $input.use_group.groups: | |
50 ,groups=${ str($input.use_group.groups).replace(",","-") } | |
51 #end if | |
52 ,persample=$input.use_group.persample | |
53 #end if | |
54 #end if | |
55 #if $count: | |
56 ,count=count.dat | |
57 #end if | |
58 #if $taxonomy: | |
59 ,taxonomy=taxonomy.dat | |
60 #end if | |
61 #if $size: | |
62 ,size=$size | |
63 #end if | |
64 )' | |
65 | sed 's/ //g' ## mothur trips over whitespace | |
66 | mothur | |
67 | tee mothur.out.log | |
68 ]]></command> | |
69 <inputs> | |
70 <conditional name="input"> | |
71 <param name="format" type="select" label="Select type of data to sub sample"> | |
72 <option value="fasta">FASTA</option> | |
73 <option value="list">OTU List</option> | |
74 <option value="shared">OTU Shared</option> | |
75 <option value="sabund">OTU Shared Abundance (sabund)</option> | |
76 <option value="rabund">OTU Relative Abundance (rabund)</option> | |
77 </param> | |
78 <when value="fasta"> | |
79 <param name="otu" type="data" format="fasta" label="fasta - "/> | |
80 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Group Names from your history"/> | |
81 <conditional name="use_group"> | |
82 <param name="to_filter" type="select" label="Use groups?"> | |
83 <option value="no">No</option> | |
84 <option value="yes">Yes</option> | |
85 </param> | |
86 <when value="no"/> | |
87 <when value="yes"> | |
88 <param name="group_in" type="data" format="mothur.groups" label="group - Groups"/> | |
89 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true"> | |
90 <options> | |
91 <filter type="data_meta" ref="group_in" key="groups"/> | |
92 </options> | |
93 </param> | |
94 <param name="persample" type="boolean" truevalue="true" falsevalue="false" checked="false" label="persample - select subsample of the same size from each of the groups"/> | |
95 </when> | |
96 </conditional> | |
97 </when> | |
98 <when value="list"> | |
99 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/> | |
100 <conditional name="use_group"> | |
101 <param name="to_filter" type="select" label="Use groups"> | |
102 <option value="no">No</option> | |
103 <option value="yes">Yes</option> | |
104 </param> | |
105 <when value="no"/> | |
106 <when value="yes"> | |
107 <param name="group_in" type="data" format="mothur.groups" label="group - Groups"/> | |
108 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true"> | |
109 <options> | |
110 <filter type="data_meta" ref="group_in" key="groups"/> | |
111 </options> | |
112 </param> | |
113 <param name="persample" type="boolean" truevalue="true" falsevalue="false" checked="false" label="persample - select subsample of the same size from each of the groups"/> | |
114 </when> | |
115 </conditional> | |
116 <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true"> | |
117 <expand macro="labeloptions"/> | |
118 </param> | |
119 </when> | |
120 <when value="shared"> | |
121 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/> | |
122 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true"> | |
123 <options> | |
124 <filter type="data_meta" ref="otu" key="groups"/> | |
125 </options> | |
126 </param> | |
127 <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true"> | |
128 <expand macro="labeloptions"/> | |
129 </param> | |
130 </when> | |
131 <when value="sabund"> | |
132 <param name="otu" type="data" format="mothur.sabund" label="sabund - OTU Species Abundance"/> | |
133 <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true"> | |
134 <expand macro="labeloptions"/> | |
135 </param> | |
136 </when> | |
137 <when value="rabund"> | |
138 <param name="otu" type="data" format="mothur.rabund" label="rabund - OTU Relative Abundance"/> | |
139 <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true"> | |
140 <expand macro="labeloptions"/> | |
141 </param> | |
142 </when> | |
143 </conditional> | |
144 <param name="size" type="integer" value="" min="1" optional="true" label="size - If set, the number of samples to pick"/> | |
145 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> | |
146 <param name="taxonomy" type="data" format="mothur.seq.taxonomy,mothur.ref.taxonomy" optional="true" label="taxonomy - allows a taxonomy file"/> | |
147 </inputs> | |
148 <outputs> | |
149 <expand macro="logfile-output"/> | |
150 <data name="fasta_out" format_source="otu" from_work_dir="input_otu*.subsample.*" label="${tool.name} on ${on_string}: subsample.fasta"> | |
151 <filter>input['format'] == 'fasta'</filter> | |
152 </data> | |
153 <data name="taxonomy_out" format_source="taxonomy" from_work_dir="taxonomy.subsample.dat" label="${tool.name} on ${on_string}: subsample.taxonomy"> | |
154 <filter>taxonomy</filter> | |
155 </data> | |
156 <collection name="list_out" type="list" label="${tool.name} on ${on_string}: subsample.list"> | |
157 <filter>input['format'] == 'list'</filter> | |
158 <discover_datasets pattern=".*?\.(?P<designation>.*)\.subsample\.dat" format="mothur.list"/> | |
159 </collection> | |
160 <collection name="shared_out" type="list" label="${tool.name} on ${on_string}: subsample.shared"> | |
161 <filter>input['format'] == 'shared'</filter> | |
162 <discover_datasets pattern=".*?\.(?P<designation>.*)\.subsample\.dat" format="mothur.shared"/> | |
163 </collection> | |
164 <data name="sabund_out" format="mothur.sabund" from_work_dir="input_otu*.subsample.*" label="${tool.name} on ${on_string}: subsample.sabund"> | |
165 <filter>input['format'] == 'sabund'</filter> | |
166 </data> | |
167 <data name="rabund_out" format="mothur.rabund" from_work_dir="input_otu*.subsample.*" label="${tool.name} on ${on_string}: subsample.rabund"> | |
168 <filter>input['format'] == 'rabund'</filter> | |
169 </data> | |
170 <data name="names_out" format="mothur.names" from_work_dir="input_name_in*.subsample.*" label="${tool.name} on ${on_string}: subsample.names"> | |
171 <filter>input['format'] == 'fasta' and input['name_in']</filter> | |
172 </data> | |
173 <data name="group_out" format="mothur.groups" from_work_dir="input_use_group_group_in*.subsample.*" label="${tool.name} on ${on_string}: subsample.groups"> | |
174 <filter>(input['format'] == 'fasta' or input['format'] == 'list') and input['use_group']['to_filter'] == 'yes'</filter> | |
175 </data> | |
176 </outputs> | |
177 <tests> | |
178 <test><!-- test with list --> | |
179 <param name="format" value="list"/> | |
180 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> | |
181 <output_collection name="list_out" count="36"> | |
182 <element name="0.20" ftype="mothur.list"> | |
183 <assert_contents> | |
184 <has_text text="label"/> | |
185 <has_text text="numOtus"/> | |
186 </assert_contents> | |
187 </element> | |
188 </output_collection> | |
189 <expand macro="logfile-test"/> | |
190 </test> | |
191 <test><!-- test with list and group file and label select--> | |
192 <param name="format" value="list"/> | |
193 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> | |
194 <param name="to_filter" value="yes"/> | |
195 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> | |
196 <param name="groups" value="forest,pasture"/> | |
197 <param name="label" value="0.20,0.45,0.55"/> | |
198 <output_collection name="list_out" count="3"> | |
199 <element name="0.20" ftype="mothur.list"> | |
200 <assert_contents> | |
201 <has_text text="label"/> | |
202 <has_text text="numOtus"/> | |
203 </assert_contents> | |
204 </element> | |
205 </output_collection> | |
206 <expand macro="logfile-test"/> | |
207 </test> | |
208 <test><!-- test with fasta and taxonomy --> | |
209 <param name="format" value="fasta"/> | |
210 <param name="otu" value="amazon.fasta" ftype="fasta"/> | |
211 <param name="taxonomy" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/> | |
212 <output name="fasta_out" ftype="fasta"> | |
213 <assert_contents> | |
214 <has_text text=">U"/> | |
215 </assert_contents> | |
216 </output> | |
217 <output name="taxonomy_out" ftype="mothur.seq.taxonomy"> | |
218 <assert_contents> | |
219 <has_line_matching expression="^U[0-9]+\tBacteria.*$"/> | |
220 </assert_contents> | |
221 </output> | |
222 <expand macro="logfile-test"/> | |
223 </test> | |
224 <test><!-- test with fasta and group file and name file --> | |
225 <param name="format" value="fasta"/> | |
226 <param name="otu" value="amazon.fasta" ftype="fasta"/> | |
227 <param name="to_filter" value="yes"/> | |
228 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> | |
229 <param name="groups" value="forest,pasture"/> | |
230 <param name="name_in" value="amazon1.names" ftype="mothur.names"/> | |
231 <output name="fasta_out" ftype="fasta"> | |
232 <assert_contents> | |
233 <has_text_matching expression=">U[0-9]+"/> | |
234 </assert_contents> | |
235 </output> | |
236 <output name="group_out" ftype="mothur.groups"> | |
237 <assert_contents> | |
238 <has_line_matching expression="^U[0-9]+\t(forest|pasture)$"/> | |
239 </assert_contents> | |
240 </output> | |
241 <output name="names_out" ftype="mothur.names"> | |
242 <assert_contents> | |
243 <has_line_matching expression="^U[0-9]+\tU[0-9]+$"/> | |
244 </assert_contents> | |
245 </output> | |
246 <expand macro="logfile-test"/> | |
247 </test> | |
248 <test><!-- test with shared --> | |
249 <param name="format" value="shared"/> | |
250 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> | |
251 <param name="label" value="unique,0.20"/> | |
252 <param name="groups" value="forest"/> | |
253 <output_collection name="shared_out" count="2"> | |
254 <element name="0.20" ftype="mothur.shared"> | |
255 <assert_contents> | |
256 <has_text text="label"/> | |
257 <has_text text="numOtus"/> | |
258 <has_text text="forest"/> | |
259 <not_has_text text="pasture"/> | |
260 </assert_contents> | |
261 </element> | |
262 </output_collection> | |
263 <expand macro="logfile-test"/> | |
264 </test> | |
265 <test><!-- test with rabund --> | |
266 <param name="format" value="rabund"/> | |
267 <param name="otu" value="amazon.an.rabund" ftype="mothur.rabund"/> | |
268 <output name="rabund_out" ftype="mothur.rabund"> | |
269 <assert_contents> | |
270 <has_text text="unique"/> | |
271 <has_text text="0.55"/> | |
272 </assert_contents> | |
273 </output> | |
274 <expand macro="logfile-test"/> | |
275 </test> | |
276 <test><!-- test with sabund --> | |
277 <param name="format" value="sabund"/> | |
278 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/> | |
279 <output name="sabund_out" ftype="mothur.sabund"> | |
280 <assert_contents> | |
281 <has_text text="unique"/> | |
282 <has_text text="0.55"/> | |
283 </assert_contents> | |
284 </output> | |
285 <expand macro="logfile-test"/> | |
286 </test> | |
287 </tests> | |
288 <help> | |
289 <![CDATA[ | |
290 | |
291 @MOTHUR_OVERVIEW@ | |
292 | |
293 **Command Documentation** | |
294 | |
295 The sub.sample_ command can be used as a way to normalize your data, or to create a smaller set from your original set. It takes as an input the following file types: fasta, list_, shared_, rabund_ and sabund_ to generate a new file that contains a sampling of your original file. | |
296 | |
297 .. _list: https://www.mothur.org/wiki/List_file | |
298 .. _shared: https://www.mothur.org/wiki/Shared_file | |
299 .. _rabund: https://www.mothur.org/wiki/Rabund_file | |
300 .. _sabund: https://www.mothur.org/wiki/Sabund_file | |
301 .. _sub.sample: https://www.mothur.org/wiki/Sub.sample | |
302 | |
303 ]]> | |
304 </help> | |
305 <expand macro="citations"/> | |
306 </tool> |