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comparison sub.sample.xml @ 0:8ccebd04ca3d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:51:17 -0400
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children f18e9f139d14
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-1:000000000000 0:8ccebd04ca3d
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="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$input.otu" input_otu.dat &&
11 ln -s "$count" count.dat &&
12 ln -s "$taxonomy" taxonomy.dat &&
13 #if $input.format == "fasta":
14 ln -s "$input.name_in" input_name_in.dat &&
15 #end if
16 #if ($input.format == "fasta" or $input.format == "list") and $input.use_group.to_filter == "yes":
17 ln -s "$input.use_group.group_in" input_use_group_group_in.dat &&
18 #end if
19
20 echo 'sub.sample(
21 #if $input.format == "fasta":
22 fasta=input_otu.dat
23 #if $input.name_in:
24 ,name=input_name_in.dat
25 #end if
26 #else
27 #if $input.format == "list":
28 list=input_otu.dat
29 #elif $input.format == "sabund":
30 sabund=input_otu.dat
31 #elif $input.format == "rabund":
32 rabund=input_otu.dat
33 #elif $input.format == "shared":
34 shared=input_otu.dat
35 #if $input.groups:
36 ,groups=${ str($input.groups).replace(",","-") }
37 #end if
38 #end if
39 #if $input.label:
40 ,label=${ str($input.label).replace(",","-") }
41 #end if
42 #end if
43 #if $input.format == "fasta" or $input.format == "list":
44 #if $input.use_group.to_filter == "yes":
45 ,group=input_use_group_group_in.dat
46 #if $input.use_group.groups:
47 ,groups=${ str($input.use_group.groups).replace(",","-") }
48 #end if
49 ,persample=$input.use_group.persample
50 #end if
51 #end if
52 #if $count:
53 ,count=count.dat
54 #end if
55 #if $taxonomy:
56 ,taxonomy=taxonomy.dat
57 #end if
58 #if $size:
59 ,size=$size
60 #end if
61 )'
62 | sed 's/ //g' ## mothur trips over whitespace
63 | mothur
64 ]]></command>
65 <inputs>
66 <conditional name="input">
67 <param name="format" type="select" label="Select type of data to sub sample">
68 <option value="fasta">FASTA</option>
69 <option value="list">OTU List</option>
70 <option value="shared">OTU Shared</option>
71 <option value="sabund">OTU Shared Abundance (sabund)</option>
72 <option value="rabund">OTU Relative Abundance (rabund)</option>
73 </param>
74 <when value="fasta">
75 <param name="otu" type="data" format="fasta" label="fasta - "/>
76 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Group Names from your history"/>
77 <conditional name="use_group">
78 <param name="to_filter" type="select" label="Use groups?">
79 <option value="no">No</option>
80 <option value="yes">Yes</option>
81 </param>
82 <when value="no"/>
83 <when value="yes">
84 <param name="group_in" type="data" format="mothur.groups" label="group - Groups"/>
85 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true">
86 <options>
87 <filter type="data_meta" ref="group_in" key="groups"/>
88 </options>
89 </param>
90 <param name="persample" type="boolean" truevalue="true" falsevalue="false" checked="false" label="persample - select subsample of the same size from each of the groups"/>
91 </when>
92 </conditional>
93 </when>
94 <when value="list">
95 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
96 <conditional name="use_group">
97 <param name="to_filter" type="select" label="Use groups">
98 <option value="no">No</option>
99 <option value="yes">Yes</option>
100 </param>
101 <when value="no"/>
102 <when value="yes">
103 <param name="group_in" type="data" format="mothur.groups" label="group - Groups"/>
104 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true">
105 <options>
106 <filter type="data_meta" ref="group_in" key="groups"/>
107 </options>
108 </param>
109 <param name="persample" type="boolean" truevalue="true" falsevalue="false" checked="false" label="persample - select subsample of the same size from each of the groups"/>
110 </when>
111 </conditional>
112 <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true">
113 <expand macro="labeloptions"/>
114 </param>
115 </when>
116 <when value="shared">
117 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
118 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true">
119 <options>
120 <filter type="data_meta" ref="otu" key="groups"/>
121 </options>
122 </param>
123 <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true">
124 <expand macro="labeloptions"/>
125 </param>
126 </when>
127 <when value="sabund">
128 <param name="otu" type="data" format="mothur.sabund" label="sabund - OTU Species Abundance"/>
129 <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true">
130 <expand macro="labeloptions"/>
131 </param>
132 </when>
133 <when value="rabund">
134 <param name="otu" type="data" format="mothur.rabund" label="rabund - OTU Relative Abundance"/>
135 <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true">
136 <expand macro="labeloptions"/>
137 </param>
138 </when>
139 </conditional>
140 <param name="size" type="integer" value="" min="1" optional="true" label="size - If set, the number of samples to pick"/>
141 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
142 <param name="taxonomy" type="data" format="taxonomy" optional="true" label="taxonomy - allows a taxonomy file"/>
143 </inputs>
144 <outputs>
145 <expand macro="logfile-output"/>
146 <data name="fasta_out" format_source="otu" from_work_dir="input_otu*.subsample.*" label="${tool.name} on ${on_string}: subsample.fasta">
147 <filter>input['format'] == 'fasta'</filter>
148 </data>
149 <collection name="list_out" type="list" label="${tool.name} on ${on_string}: subsample.list">
150 <filter>input['format'] == 'list'</filter>
151 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.subsample\.dat" format="mothur.list"/>
152 </collection>
153 <collection name="shared_out" type="list" label="${tool.name} on ${on_string}: subsample.shared">
154 <filter>input['format'] == 'shared'</filter>
155 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.subsample\.dat" format="mothur.shared"/>
156 </collection>
157 <data name="sabund_out" format="mothur.sabund" from_work_dir="input_otu*.subsample.*" label="${tool.name} on ${on_string}: subsample.sabund">
158 <filter>input['format'] == 'sabund'</filter>
159 </data>
160 <data name="rabund_out" format="mothur.rabund" from_work_dir="input_otu*.subsample.*" label="${tool.name} on ${on_string}: subsample.rabund">
161 <filter>input['format'] == 'rabund'</filter>
162 </data>
163 <data name="names_out" format="mothur.names" from_work_dir="input_name_in*.subsample.*" label="${tool.name} on ${on_string}: subsample.names">
164 <filter>input['format'] == 'fasta' and input['name_in']</filter>
165 </data>
166 <data name="group_out" format="mothur.groups" from_work_dir="input_use_group_group_in*.subsample.*" label="${tool.name} on ${on_string}: subsample.groups">
167 <filter>(input['format'] == 'fasta' or input['format'] == 'list') and input['use_group']['to_filter'] == 'yes'</filter>
168 </data>
169 </outputs>
170 <tests>
171 <test><!-- test with list -->
172 <param name="format" value="list"/>
173 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
174 <output_collection name="list_out" count="36">
175 <element name="0.20" ftype="mothur.list">
176 <assert_contents>
177 <has_text text="label"/>
178 <has_text text="numOtus"/>
179 </assert_contents>
180 </element>
181 </output_collection>
182 <expand macro="logfile-test"/>
183 </test>
184 <test><!-- test with list and group file and label select-->
185 <param name="format" value="list"/>
186 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
187 <param name="to_filter" value="yes"/>
188 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
189 <param name="groups" value="forest,pasture"/>
190 <param name="label" value="0.20,0.45,0.55"/>
191 <output_collection name="list_out" count="3">
192 <element name="0.20" ftype="mothur.list">
193 <assert_contents>
194 <has_text text="label"/>
195 <has_text text="numOtus"/>
196 </assert_contents>
197 </element>
198 </output_collection>
199 <expand macro="logfile-test"/>
200 </test>
201 <test><!-- test with fasta -->
202 <param name="format" value="fasta"/>
203 <param name="otu" value="amazon.fasta" ftype="fasta"/>
204 <output name="fasta_out" ftype="fasta">
205 <assert_contents>
206 <has_text text=">U"/>
207 </assert_contents>
208 </output>
209 <expand macro="logfile-test"/>
210 </test>
211 <test><!-- test with fasta and group file and name file -->
212 <param name="format" value="fasta"/>
213 <param name="otu" value="amazon.fasta" ftype="fasta"/>
214 <param name="to_filter" value="yes"/>
215 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
216 <param name="groups" value="forest,pasture"/>
217 <param name="name_in" value="amazon1.names" ftype="mothur.names"/>
218 <output name="fasta_out" ftype="fasta">
219 <assert_contents>
220 <has_text_matching expression=">U[0-9]+"/>
221 </assert_contents>
222 </output>
223 <output name="group_out" ftype="mothur.groups">
224 <assert_contents>
225 <has_line_matching expression="^U[0-9]+\t(forest|pasture)$"/>
226 </assert_contents>
227 </output>
228 <output name="names_out" ftype="mothur.names">
229 <assert_contents>
230 <has_line_matching expression="^U[0-9]+\tU[0-9]+$"/>
231 </assert_contents>
232 </output>
233 <expand macro="logfile-test"/>
234 </test>
235 <test><!-- test with shared -->
236 <param name="format" value="shared"/>
237 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
238 <param name="label" value="unique,0.20"/>
239 <param name="groups" value="forest"/>
240 <output_collection name="shared_out" count="2">
241 <element name="0.20" ftype="mothur.shared">
242 <assert_contents>
243 <has_text text="label"/>
244 <has_text text="numOtus"/>
245 <has_text text="forest"/>
246 <not_has_text text="pasture"/>
247 </assert_contents>
248 </element>
249 </output_collection>
250 <expand macro="logfile-test"/>
251 </test>
252 <test><!-- test with rabund -->
253 <param name="format" value="rabund"/>
254 <param name="otu" value="amazon.an.rabund" ftype="mothur.rabund"/>
255 <output name="rabund_out" ftype="mothur.rabund">
256 <assert_contents>
257 <has_text text="unique"/>
258 <has_text text="0.55"/>
259 </assert_contents>
260 </output>
261 <expand macro="logfile-test"/>
262 </test>
263 <test><!-- test with sabund -->
264 <param name="format" value="sabund"/>
265 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
266 <output name="sabund_out" ftype="mothur.sabund">
267 <assert_contents>
268 <has_text text="unique"/>
269 <has_text text="0.55"/>
270 </assert_contents>
271 </output>
272 <expand macro="logfile-test"/>
273 </test>
274 </tests>
275 <help>
276 <![CDATA[
277
278 @MOTHUR_OVERVIEW@
279
280 **Command Documenation**
281
282 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.
283
284 .. _list: http://www.mothur.org/wiki/List_file
285 .. _shared: http://www.mothur.org/wiki/Shared_file
286 .. _rabund: http://www.mothur.org/wiki/Rabund_file
287 .. _sabund: http://www.mothur.org/wiki/Sabund_file
288 .. _sub.sample: http://www.mothur.org/wiki/Sub.sample
289
290 ]]>
291 </help>
292 <expand macro="citations"/>
293 </tool>