Mercurial > repos > iuc > mothur_split_abund

comparison split.abund.xml @ 0:2077ddb27f4c 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 16:50:46 -0400
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children 59ab81a8d28d
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-1:000000000000 0:2077ddb27f4c
1 <tool profile="16.07" id="mothur_split_abund" name="Split.abund" version="@WRAPPER_VERSION@.0">
2 <description>Separate sequences into rare and abundant groups</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 "$fasta" fasta.dat &&
11 ln -s "$search.input" search_input.dat &&
12 #if $split.dosplit == "yes":
13 ln -s "$split.group" split_group.dat &&
14 #end if
15
16 echo 'split.abund(
17 fasta=fasta.dat,
18 #if $search.type == "list":
19 list=search_input.dat,
20 #if $search.label:
21 label=${ str($search.label).replace(",","-") },
22 #end if
23 #elif $search.type == "name":
24 name=search_input.dat,
25 #else
26 count=search_input.dat,
27 #end if
28 #if $split.dosplit == "yes":
29 #if $split.group:
30 group=split_group.dat,
31 #end if
32 #if $split.groups:
33 groups=${ str($split.groups).replace(",","-") },
34 #end if
35 #end if
36 accnos=$accnos,
37 cutoff=$cutoff
38 )'
39 | sed 's/ //g' ## mothur trips over whitespace
40 | mothur
41 ]]></command>
42 <inputs>
43 <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
44 <param name="cutoff" type="integer" value="10" min="0" label="cutoff - Cutoff parameter is used to qualify what is abundant and rare."/>
45 <conditional name="search">
46 <param name="type" type="select" label="Type to screen" help="">
47 <option value="list">OTU List</option>
48 <option value="name">Name reference</option>
49 <option value="count">Count file</option>
50 </param>
51 <when value="name">
52 <param name="input" type="data" format="mothur.names" label="name - Name reference"/>
53 </when>
54 <when value="list">
55 <param name="input" type="data" format="mothur.list" label="list - OTU List"/>
56 <param name="label" type="select" label="label - OTU Labels" multiple="true" help="Select OTU Labels to filter out all but selected labels">
57 <options>
58 <filter type="data_meta" ref="input" key="labels"/>
59 </options>
60 </param>
61 </when>
62 <when value="count">
63 <param name="input" type="data" format="mothur.count_table" label="count - count_table file"/>
64 </when>
65 </conditional>
66 <conditional name="split">
67 <param name="dosplit" type="select" label="Parse a group file into abundant and rare groups? (only possible if name or list file supplied)" help="">
68 <option value="no" selected="true">No</option>
69 <option value="yes">Yes</option>
70 </param>
71 <when value="yes">
72 <param name="group" type="data" format="mothur.groups" label="group - Group dataset"/>
73 <param name="groups" type="select" multiple="true" label="groups - Group Selection">
74 <options>
75 <filter type="data_meta" ref="group" key="groups"/>
76 </options>
77 </param>
78 </when>
79 <when value="no"/>
80 </conditional>
81 <param name="accnos" type="boolean" truevalue="true" falsevalue="false" checked="false" label="accnos - Produce rare and abundant Accession outputs"/>
82 </inputs>
83 <outputs>
84 <expand macro="logfile-output"/>
85 <data name="abund_fasta" format_source="fasta" from_work_dir="*abund.fasta" label="${tool.name} on ${on_string}: abund.fasta">
86 <filter>search['type'] != 'list'</filter>
87 </data>
88 <data name="rare_fasta" format_source="fasta" from_work_dir="*rare.fasta" label="${tool.name} on ${on_string}: rare.fasta">
89 <filter>search['type'] != 'list'</filter>
90 </data>
91 <data name="abund_groups" format="mothur.groups" label="${tool.name} on ${on_string}: abund.groups">
92 <filter>search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
93 </data>
94 <data name="rare_groups" format="mothur.groups" label="${tool.name} on ${on_string}: rare.groups">
95 <filter>search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
96 </data>
97 <data name="abund_names" format="mothur.names" from_work_dir="search_input*.abund.names" label="${tool.name} on ${on_string}: abund.names">
98 <filter>search['type'] == 'name'</filter>
99 </data>
100 <data name="rare_names" format="mothur.names" from_work_dir="search_input*.rare.names" label="${tool.name} on ${on_string}: rare.fasta">
101 <filter>search['type'] == 'name'</filter>
102 </data>
103 <data name="abund_count" format="mothur.count_table" from_work_dir="*.abund.count_table" label="${tool.name} on ${on_string}: abund.count_table">
104 <filter>search['type'] == 'count'</filter>
105 </data>
106 <data name="rare_count" format="mothur.count_table" from_work_dir="*.rare.count_table" label="${tool.name} on ${on_string}: rare.count_table">
107 <filter>search['type'] == 'count'</filter>
108 </data>
109 <data name="abund_accnos" format="mothur.accnos" from_work_dir="*abund.accnos" label="${tool.name} on ${on_string}: abund.accnos">
110 <filter>search['type'] != 'list' and accnos</filter>
111 </data>
112 <data name="rare_accnos" format="mothur.accnos" from_work_dir="*rare.accnos" label="${tool.name} on ${on_string}: rare.accnos">
113 <filter>search['type'] != 'list' and accnos</filter>
114 </data>
115 <collection name="abund_fasta_coll" type="list" label="${tool.name} on ${on_string}: abund.fasta">
116 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.abund\.fasta" format="fasta"/>
117 <filter>search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
118 </collection>
119 <collection name="rare_fasta_coll" type="list" label="${tool.name} on ${on_string}: rare.fasta">
120 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rare\.fasta" format="fasta"/>
121 <filter>search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes')</filter>
122 </collection>
123 <collection name="abund_list_coll" type="list" label="${tool.name} on ${on_string}: abund.list">
124 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.abund\.list" format="mothur.list"/>
125 <filter>search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
126 </collection>
127 <collection name="rare_list_coll" type="list" label="${tool.name} on ${on_string}: rare.list">
128 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rare\.list" format="mothur.list"/>
129 <filter>search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
130 </collection>
131 <collection name="abund_accnos_coll" type="list" label="${tool.name} on ${on_string}: abund.accnos">
132 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.abund\.accnos" format="mothur.accnos"/>
133 <filter>(search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes')) and accnos</filter>
134 </collection>
135 <collection name="rare_accnos_coll" type="list" label="${tool.name} on ${on_string}: rare.accnos">
136 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rare\.accnos" format="mothur.accnos"/>
137 <filter>(search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes')) and accnos</filter>
138 </collection>
139 <collection name="abund_groups_coll" type="list" label="${tool.name} on ${on_string}: abund.groups">
140 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.abund\.groups" format="mothur.groups"/>
141 <filter>search['type'] != 'count' and split['dosplit'] == 'yes'</filter>
142 </collection>
143 <collection name="rare_groups_coll" type="list" label="${tool.name} on ${on_string}: rare.groups">
144 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rare\.groups" format="mothur.groups"/>
145 <filter>search['type'] != 'count' and split['dosplit'] == 'yes'</filter>
146 </collection>
147 <collection name="abund_names_coll" type="list" label="${tool.name} on ${on_string}: abund.names">
148 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.abund\.names" format="mothur.names"/>
149 <filter>search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
150 </collection>
151 <collection name="rare_names_coll" type="list" label="${tool.name} on ${on_string}: rare.names">
152 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rare\.names" format="mothur.names"/>
153 <filter>search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
154 </collection>
155 </outputs>
156 <tests>
157 <test><!-- test with count table -->
158 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
159 <param name="type" value="count"/>
160 <param name="input" value="amazon.count_table" ftype="mothur.count_table"/>
161 <param name="cutoff" value="1"/>
162 <param name="accnos" value="true"/>
163 <output name="abund_fasta" md5="3c147ce7224bc8c8602d2ccfe4b6eae7" ftype="fasta"/>
164 <output name="rare_fasta" md5="bff57d4585fe4e6d8b86c949f3e17e1a" ftype="fasta"/>
165 <output name="abund_count" md5="288e5222f3d454b67761fca3c8c944b1" ftype="mothur.count_table"/>
166 <output name="rare_count" md5="dc7be856861ef53faa73a5312b0661c3" ftype="mothur.count_table"/>
167 <output name="abund_accnos" md5="47c918c965d41fea12bad748afe60833" ftype="mothur.accnos"/>
168 <output name="rare_accnos" md5="3537f34f96d276e72e03f6d6a4994fd9" ftype="mothur.accnos"/>
169 <expand macro="logfile-test"/>
170 </test>
171 <test><!-- test with name file and accnos output -->
172 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
173 <param name="type" value="name"/>
174 <param name="input" value="amazon.names" ftype="mothur.names"/>
175 <param name="cutoff" value="1"/>
176 <param name="accnos" value="true"/>
177 <output name="abund_fasta" md5="3c147ce7224bc8c8602d2ccfe4b6eae7" ftype="fasta"/>
178 <output name="rare_fasta" md5="bff57d4585fe4e6d8b86c949f3e17e1a" ftype="fasta"/>
179 <output name="abund_names" md5="41560e422d53c83cb482ef868409136c" ftype="mothur.names"/>
180 <output name="rare_names" md5="12527477b2c1891c9278f417a5ece45d" ftype="mothur.names"/>
181 <output name="abund_accnos" md5="47c918c965d41fea12bad748afe60833" ftype="mothur.accnos"/>
182 <output name="rare_accnos" md5="3537f34f96d276e72e03f6d6a4994fd9" ftype="mothur.accnos"/>
183 <expand macro="logfile-test"/>
184 </test>
185 <test><!-- test with name file and accnos output with groups-->
186 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
187 <param name="type" value="name"/>
188 <param name="input" value="amazon.names" ftype="mothur.names"/>
189 <param name="cutoff" value="1"/>
190 <param name="accnos" value="true"/>
191 <param name="dosplit" value="yes"/>
192 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
193 <param name="groups" value="forest,pasture"/>
194 <output_collection name="abund_fasta_coll" count="2">
195 <element name="forest" md5="8d90da3c099450e31de006548e8f458c" ftype="fasta"/>
196 </output_collection>
197 <output_collection name="rare_fasta_coll" count="2">
198 <element name="forest" md5="4459f7ee4c46ccf0ce33f5694ac1ca49" ftype="fasta"/>
199 </output_collection>
200 <output_collection name="abund_names_coll" count="2">
201 <element name="pasture" md5="d45b69987a0294c87fab358bbb71cd29" ftype="mothur.names"/>
202 </output_collection>
203 <output_collection name="rare_names_coll" count="2">
204 <element name="pasture" md5="fc5d939ceca270be00b39d5323c1a79f" ftype="mothur.names"/>
205 </output_collection>
206 <output_collection name="abund_accnos_coll" count="2">
207 <element name="forest" md5="597a2cc6d2da897434ec9d2c11489d0a" ftype="mothur.accnos"/>
208 </output_collection>
209 <output_collection name="rare_accnos_coll" count="2">
210 <element name="forest" md5="20f8e54d68bf225f405258942e0cb5ac" ftype="mothur.accnos"/>
211 </output_collection>
212 <output_collection name="abund_groups_coll" count="2">
213 <element name="pasture" md5="46ac8394df6b3376b41619b07720ee18" ftype="mothur.groups"/>
214 </output_collection>
215 <output_collection name="rare_groups_coll" count="2">
216 <element name="pasture" md5="5907bd7fe874a29fcc57930ecb0f65d1" ftype="mothur.groups"/>
217 </output_collection>
218 <expand macro="logfile-test"/>
219 </test>
220 <test><!-- test with list -->
221 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
222 <param name="type" value="list"/>
223 <param name="input" value="amazon.an.list" ftype="mothur.list"/>
224 <param name="cutoff" value="2"/>
225 <param name="accnos" value="true"/>
226 <param name="dosplit" value="yes"/>
227 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
228 <param name="groups" value="forest,pasture"/>
229 <output_collection name="abund_fasta_coll" count="72">
230 <element name="0.05.forest" md5="1860c0cf143a2b7adc93c88418ed3559" ftype="fasta"/>
231 </output_collection>
232 <output_collection name="rare_fasta_coll" count="72">
233 <element name="0.05.pasture" md5="7c9ca6c2f3e2eb5c3d38c30963b3d976" ftype="fasta"/>
234 </output_collection>
235 <output_collection name="abund_list_coll" count="72">
236 <element name="forest.0.05" md5="8a0843911399171a73afbc0374065fd0" ftype="mothur.list"/>
237 </output_collection>
238 <output_collection name="rare_list_coll" count="72">
239 <element name="pasture.0.05" md5="b7dc64a835d318852dbadc0c3379d0bb" ftype="mothur.list"/>
240 </output_collection>
241 <output_collection name="abund_accnos_coll" count="72">
242 <element name="0.05.forest" md5="e9f9b640ca00c11cba5420069c916b12" ftype="mothur.accnos"/>
243 </output_collection>
244 <output_collection name="rare_accnos_coll" count="72">
245 <element name="0.05.pasture" md5="e866c488171950bb38e7ba4c8f2982c1" ftype="mothur.accnos"/>
246 </output_collection>
247 <output_collection name="abund_groups_coll" count="72">
248 <element name="0.05.forest" md5="fd404451b15195cadb637751a463a077" ftype="mothur.groups"/>
249 </output_collection>
250 <output_collection name="rare_groups_coll" count="72">
251 <element name="0.05.pasture" md5="ddcf8bc26a0815fd366deceec64133ee" ftype="mothur.groups"/>
252 </output_collection>
253 <expand macro="logfile-test"/>
254 </test>
255 <test><!-- test with list and label and group select-->
256 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
257 <param name="type" value="list"/>
258 <param name="input" value="amazon.an.list" ftype="mothur.list"/>
259 <param name="cutoff" value="2"/>
260 <param name="label" value="0.05,0.22"/>
261 <param name="accnos" value="true"/>
262 <param name="dosplit" value="yes"/>
263 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
264 <param name="groups" value="forest,pasture"/>
265 <output_collection name="abund_fasta_coll" count="4">
266 <element name="0.05.pasture" md5="51327cbf0c66c9c3074ca3456b021ead" ftype="fasta"/>
267 </output_collection>
268 <output_collection name="rare_fasta_coll" count="4">
269 <element name="0.05.pasture" md5="7c9ca6c2f3e2eb5c3d38c30963b3d976" ftype="fasta"/>
270 </output_collection>
271 <output_collection name="abund_list_coll" count="4">
272 <element name="forest.0.05" md5="8a0843911399171a73afbc0374065fd0" ftype="mothur.list"/>
273 </output_collection>
274 <output_collection name="rare_list_coll" count="4">
275 <element name="forest.0.05" md5="f79b02e37dbd7a7f76a60c269571396f" ftype="mothur.list"/>
276 </output_collection>
277 <output_collection name="abund_accnos_coll" count="4">
278 <element name="0.05.pasture" md5="3a875836ffebfeb037cd761ea1d0607e" ftype="mothur.accnos"/>
279 </output_collection>
280 <output_collection name="rare_accnos_coll" count="4">
281 <element name="0.05.pasture" md5="e866c488171950bb38e7ba4c8f2982c1" ftype="mothur.accnos"/>
282 </output_collection>
283 <output_collection name="abund_groups_coll" count="4">
284 <element name="0.05.forest" md5="fd404451b15195cadb637751a463a077" ftype="mothur.groups"/>
285 </output_collection>
286 <output_collection name="rare_groups_coll" count="4">
287 <element name="0.05.forest" md5="53a2f24a4d69f92661b94bc4b813ce69" ftype="mothur.groups"/>
288 </output_collection>
289 <expand macro="logfile-test"/>
290 </test>
291 </tests>
292 <help>
293 <![CDATA[
294
295 @MOTHUR_OVERVIEW@
296
297 **Command Documenation**
298
299 The split.abund_ command reads a fasta file and a list_ or a name_ file and splits the sequences into rare and abundant groups.
300
301 .. _list: http://www.mothur.org/wiki/List_file
302 .. _name: http://www.mothur.org/wiki/Name_file
303 .. _split.abund: http://www.mothur.org/wiki/Split.abund
304 ]]>
305 </help>
306 <expand macro="citations"/>
307 </tool>