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comparison sub.sample.xml @ 0:be6c106b1960 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:55:16 -0400
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children 46d13e8c60ba
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-1:000000000000 0:be6c106b1960
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 ${on_string}: subsample.list">
157 <filter>input['format'] == 'list'</filter>
158 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.subsample\.dat" format="mothur.list"/>
159 </collection>
160 <collection name="shared_out" type="list" label="${tool.name} on ${on_string}: subsample.shared">
161 <filter>input['format'] == 'shared'</filter>
162 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.subsample\.dat" format="mothur.shared"/>
163 </collection>
164 <data name="sabund_out" format="mothur.sabund" from_work_dir="input_otu*.subsample.*" label="${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>