Mercurial > repos > iuc > mothur_sub_sample

comparison sub.sample.xml @ 2:46d13e8c60ba 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 22:24:53 -0400
parents be6c106b1960
children 2986f7b01e74
comparison
equal deleted inserted replaced
1:e866e31f6da3 2:46d13e8c60ba
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 "$input.otu" input_otu.dat && 13 ln -s '$input.otu' input_otu.dat &&
14 ln -s "$count" count.dat && 14 ln -s '$count' count.dat &&
15 ln -s "$taxonomy" taxonomy.dat && 15 ln -s '$taxonomy' taxonomy.dat &&
16 #if $input.format == "fasta": 16 #if $input.format == "fasta":
17 ln -s "$input.name_in" input_name_in.dat && 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 $input.name_in:
27 ,name=input_name_in.dat
18 #end if 28 #end if
19 #if ($input.format == "fasta" or $input.format == "list") and $input.use_group.to_filter == "yes": 29 #else
20 ln -s "$input.use_group.group_in" input_use_group_group_in.dat && 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
21 #end if 41 #end if
22 42 #if $input.label:
23 echo 'sub.sample( 43 ,label=${ str($input.label).replace(",","-") }
24 #if $input.format == "fasta": 44 #end if
25 fasta=input_otu.dat 45 #end if
26 #if $input.name_in: 46 #if $input.format == "fasta" or $input.format == "list":
27 ,name=input_name_in.dat 47 #if $input.use_group.to_filter == "yes":
28 #end if 48 ,group=input_use_group_group_in.dat
29 #else 49 #if $input.use_group.groups:
30 #if $input.format == "list": 50 ,groups=${ str($input.use_group.groups).replace(",","-") }
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 51 #end if
46 #if $input.format == "fasta" or $input.format == "list": 52 ,persample=$input.use_group.persample
47 #if $input.use_group.to_filter == "yes": 53 #end if
48 ,group=input_use_group_group_in.dat 54 #end if
49 #if $input.use_group.groups: 55 #if $count:
50 ,groups=${ str($input.use_group.groups).replace(",","-") } 56 ,count=count.dat
51 #end if 57 #end if
52 ,persample=$input.use_group.persample 58 #if $taxonomy:
53 #end if 59 ,taxonomy=taxonomy.dat
54 #end if 60 #end if
55 #if $count: 61 #if $size:
56 ,count=count.dat 62 ,size=$size
57 #end if 63 #end if
58 #if $taxonomy: 64 )'
59 ,taxonomy=taxonomy.dat 65 | sed 's/ //g' ## mothur trips over whitespace
60 #end if 66 | mothur
61 #if $size: 67 | tee mothur.out.log
62 ,size=$size
63 #end if
64 )'
65 | sed 's/ //g' ## mothur trips over whitespace
66 | mothur
67 | tee mothur.out.log
68 ]]></command> 68 ]]></command>
69 <inputs> 69 <inputs>
70 <conditional name="input"> 70 <conditional name="input">
71 <param name="format" type="select" label="Select type of data to sub sample"> 71 <param name="format" type="select" label="Select type of data to sub sample">
72 <option value="fasta">FASTA</option> 72 <option value="fasta">FASTA</option>
142 </when> 142 </when>
143 </conditional> 143 </conditional>
144 <param name="size" type="integer" value="" min="1" optional="true" label="size - If set, the number of samples to pick"/> 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"/> 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"/> 146 <param name="taxonomy" type="data" format="mothur.seq.taxonomy,mothur.ref.taxonomy" optional="true" label="taxonomy - allows a taxonomy file"/>
147 <expand macro="param-savelog"/>
147 </inputs> 148 </inputs>
148 <outputs> 149 <outputs>
149 <expand macro="logfile-output"/> 150 <expand macro="logfile-output"/>
150 <data name="fasta_out" format_source="otu" from_work_dir="input_otu*.subsample.*" label="${tool.name} on ${on_string}: subsample.fasta"> 151 <data name="fasta_out" format_source="otu" from_work_dir="input_otu*.subsample.*" label="${tool.name} on ${on_string}: subsample.fasta">
151 <filter>input['format'] == 'fasta'</filter> 152 <filter>input['format'] == 'fasta'</filter>
184 <has_text text="label"/> 185 <has_text text="label"/>
185 <has_text text="numOtus"/> 186 <has_text text="numOtus"/>
186 </assert_contents> 187 </assert_contents>
187 </element> 188 </element>
188 </output_collection> 189 </output_collection>
190 <param name="savelog" value="true"/>
189 <expand macro="logfile-test"/> 191 <expand macro="logfile-test"/>
190 </test> 192 </test>
191 <test><!-- test with list and group file and label select--> 193 <test><!-- test with list and group file and label select-->
192 <param name="format" value="list"/> 194 <param name="format" value="list"/>
193 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 195 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
201 <has_text text="label"/> 203 <has_text text="label"/>
202 <has_text text="numOtus"/> 204 <has_text text="numOtus"/>
203 </assert_contents> 205 </assert_contents>
204 </element> 206 </element>
205 </output_collection> 207 </output_collection>
208 <param name="savelog" value="true"/>
206 <expand macro="logfile-test"/> 209 <expand macro="logfile-test"/>
207 </test> 210 </test>
208 <test><!-- test with fasta and taxonomy --> 211 <test><!-- test with fasta and taxonomy -->
209 <param name="format" value="fasta"/> 212 <param name="format" value="fasta"/>
210 <param name="otu" value="amazon.fasta" ftype="fasta"/> 213 <param name="otu" value="amazon.fasta" ftype="fasta"/>
217 <output name="taxonomy_out" ftype="mothur.seq.taxonomy"> 220 <output name="taxonomy_out" ftype="mothur.seq.taxonomy">
218 <assert_contents> 221 <assert_contents>
219 <has_line_matching expression="^U[0-9]+\tBacteria.*$"/> 222 <has_line_matching expression="^U[0-9]+\tBacteria.*$"/>
220 </assert_contents> 223 </assert_contents>
221 </output> 224 </output>
225 <param name="savelog" value="true"/>
222 <expand macro="logfile-test"/> 226 <expand macro="logfile-test"/>
223 </test> 227 </test>
224 <test><!-- test with fasta and group file and name file --> 228 <test><!-- test with fasta and group file and name file -->
225 <param name="format" value="fasta"/> 229 <param name="format" value="fasta"/>
226 <param name="otu" value="amazon.fasta" ftype="fasta"/> 230 <param name="otu" value="amazon.fasta" ftype="fasta"/>
241 <output name="names_out" ftype="mothur.names"> 245 <output name="names_out" ftype="mothur.names">
242 <assert_contents> 246 <assert_contents>
243 <has_line_matching expression="^U[0-9]+\tU[0-9]+$"/> 247 <has_line_matching expression="^U[0-9]+\tU[0-9]+$"/>
244 </assert_contents> 248 </assert_contents>
245 </output> 249 </output>
250 <param name="savelog" value="true"/>
246 <expand macro="logfile-test"/> 251 <expand macro="logfile-test"/>
247 </test> 252 </test>
248 <test><!-- test with shared --> 253 <test><!-- test with shared -->
249 <param name="format" value="shared"/> 254 <param name="format" value="shared"/>
250 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 255 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
258 <has_text text="forest"/> 263 <has_text text="forest"/>
259 <not_has_text text="pasture"/> 264 <not_has_text text="pasture"/>
260 </assert_contents> 265 </assert_contents>
261 </element> 266 </element>
262 </output_collection> 267 </output_collection>
268 <param name="savelog" value="true"/>
263 <expand macro="logfile-test"/> 269 <expand macro="logfile-test"/>
264 </test> 270 </test>
265 <test><!-- test with rabund --> 271 <test><!-- test with rabund -->
266 <param name="format" value="rabund"/> 272 <param name="format" value="rabund"/>
267 <param name="otu" value="amazon.an.rabund" ftype="mothur.rabund"/> 273 <param name="otu" value="amazon.an.rabund" ftype="mothur.rabund"/>
269 <assert_contents> 275 <assert_contents>
270 <has_text text="unique"/> 276 <has_text text="unique"/>
271 <has_text text="0.55"/> 277 <has_text text="0.55"/>
272 </assert_contents> 278 </assert_contents>
273 </output> 279 </output>
280 <param name="savelog" value="true"/>
274 <expand macro="logfile-test"/> 281 <expand macro="logfile-test"/>
275 </test> 282 </test>
276 <test><!-- test with sabund --> 283 <test><!-- test with sabund -->
277 <param name="format" value="sabund"/> 284 <param name="format" value="sabund"/>
278 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/> 285 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
280 <assert_contents> 287 <assert_contents>
281 <has_text text="unique"/> 288 <has_text text="unique"/>
282 <has_text text="0.55"/> 289 <has_text text="0.55"/>
283 </assert_contents> 290 </assert_contents>
284 </output> 291 </output>
292 <param name="savelog" value="true"/>
285 <expand macro="logfile-test"/> 293 <expand macro="logfile-test"/>
286 </test> 294 </test>
287 </tests> 295 </tests>
288 <help> 296 <help><![CDATA[
289 <![CDATA[
290 297
291 @MOTHUR_OVERVIEW@ 298 @MOTHUR_OVERVIEW@
292 299
293 **Command Documentation** 300 **Command Documentation**
294 301
298 .. _shared: https://www.mothur.org/wiki/Shared_file 305 .. _shared: https://www.mothur.org/wiki/Shared_file
299 .. _rabund: https://www.mothur.org/wiki/Rabund_file 306 .. _rabund: https://www.mothur.org/wiki/Rabund_file
300 .. _sabund: https://www.mothur.org/wiki/Sabund_file 307 .. _sabund: https://www.mothur.org/wiki/Sabund_file
301 .. _sub.sample: https://www.mothur.org/wiki/Sub.sample 308 .. _sub.sample: https://www.mothur.org/wiki/Sub.sample
302 309
303 ]]> 310 ]]></help>
304 </help>
305 <expand macro="citations"/> 311 <expand macro="citations"/>
306 </tool> 312 </tool>