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comparison split.abund.xml @ 0:b15d9a2d2311 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 04:59:16 -0400
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children 407a5352f0ec
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-1:000000000000 0:b15d9a2d2311
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="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$fasta" fasta.dat &&
14 ln -s "$search.input" search_input.dat &&
15 #if $split.dosplit == "yes":
16 ln -s "$split.group" split_group.dat &&
17 #end if
18
19 echo 'split.abund(
20 fasta=fasta.dat,
21 #if $search.type == "list":
22 list=search_input.dat,
23 #if $search.label:
24 label=${ str($search.label).replace(",","-") },
25 #end if
26 #elif $search.type == "name":
27 name=search_input.dat,
28 #else
29 count=search_input.dat,
30 #end if
31 #if $split.dosplit == "yes":
32 #if $split.group:
33 group=split_group.dat,
34 #end if
35 #if $split.groups:
36 groups=${ str($split.groups).replace(",","-") },
37 #end if
38 #end if
39 accnos=$accnos,
40 cutoff=$cutoff
41 )'
42 | sed 's/ //g' ## mothur trips over whitespace
43 | mothur
44 | tee mothur.out.log
45 ]]></command>
46 <inputs>
47 <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
48 <param name="cutoff" type="integer" value="10" min="0" label="cutoff - Cutoff parameter is used to qualify what is abundant and rare."/>
49 <conditional name="search">
50 <param name="type" type="select" label="Type to screen" help="">
51 <option value="list">OTU List</option>
52 <option value="name">Name reference</option>
53 <option value="count">Count file</option>
54 </param>
55 <when value="name">
56 <param name="input" type="data" format="mothur.names" label="name - Name reference"/>
57 </when>
58 <when value="list">
59 <param name="input" type="data" format="mothur.list" label="list - OTU List"/>
60 <param name="label" type="select" label="label - OTU Labels" multiple="true" help="Select OTU Labels to filter out all but selected labels">
61 <options>
62 <filter type="data_meta" ref="input" key="labels"/>
63 </options>
64 </param>
65 </when>
66 <when value="count">
67 <param name="input" type="data" format="mothur.count_table" label="count - count_table file"/>
68 </when>
69 </conditional>
70 <conditional name="split">
71 <param name="dosplit" type="select" label="Parse a group file into abundant and rare groups? (only possible if name or list file supplied)" help="">
72 <option value="no" selected="true">No</option>
73 <option value="yes">Yes</option>
74 </param>
75 <when value="yes">
76 <param name="group" type="data" format="mothur.groups" label="group - Group dataset"/>
77 <param name="groups" type="select" multiple="true" label="groups - Group Selection">
78 <options>
79 <filter type="data_meta" ref="group" key="groups"/>
80 </options>
81 </param>
82 </when>
83 <when value="no"/>
84 </conditional>
85 <param name="accnos" type="boolean" truevalue="true" falsevalue="false" checked="false" label="accnos - Produce rare and abundant Accession outputs"/>
86 </inputs>
87 <outputs>
88 <expand macro="logfile-output"/>
89 <data name="abund_fasta" format_source="fasta" from_work_dir="*abund.fasta" label="${tool.name} on ${on_string}: abund.fasta">
90 <filter>search['type'] != 'list'</filter>
91 </data>
92 <data name="rare_fasta" format_source="fasta" from_work_dir="*rare.fasta" label="${tool.name} on ${on_string}: rare.fasta">
93 <filter>search['type'] != 'list'</filter>
94 </data>
95 <data name="abund_groups" format="mothur.groups" label="${tool.name} on ${on_string}: abund.groups">
96 <filter>search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
97 </data>
98 <data name="rare_groups" format="mothur.groups" label="${tool.name} on ${on_string}: rare.groups">
99 <filter>search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
100 </data>
101 <data name="abund_names" format="mothur.names" from_work_dir="search_input*.abund.names" label="${tool.name} on ${on_string}: abund.names">
102 <filter>search['type'] == 'name'</filter>
103 </data>
104 <data name="rare_names" format="mothur.names" from_work_dir="search_input*.rare.names" label="${tool.name} on ${on_string}: rare.fasta">
105 <filter>search['type'] == 'name'</filter>
106 </data>
107 <data name="abund_count" format="mothur.count_table" from_work_dir="*.abund.count_table" label="${tool.name} on ${on_string}: abund.count_table">
108 <filter>search['type'] == 'count'</filter>
109 </data>
110 <data name="rare_count" format="mothur.count_table" from_work_dir="*.rare.count_table" label="${tool.name} on ${on_string}: rare.count_table">
111 <filter>search['type'] == 'count'</filter>
112 </data>
113 <data name="abund_accnos" format="mothur.accnos" from_work_dir="*abund.accnos" label="${tool.name} on ${on_string}: abund.accnos">
114 <filter>search['type'] != 'list' and accnos</filter>
115 </data>
116 <data name="rare_accnos" format="mothur.accnos" from_work_dir="*rare.accnos" label="${tool.name} on ${on_string}: rare.accnos">
117 <filter>search['type'] != 'list' and accnos</filter>
118 </data>
119 <collection name="abund_fasta_coll" type="list" label="${tool.name} on ${on_string}: abund.fasta">
120 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.abund\.fasta" format="fasta"/>
121 <filter>search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
122 </collection>
123 <collection name="rare_fasta_coll" type="list" label="${tool.name} on ${on_string}: rare.fasta">
124 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rare\.fasta" format="fasta"/>
125 <filter>search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes')</filter>
126 </collection>
127 <collection name="abund_list_coll" type="list" label="${tool.name} on ${on_string}: abund.list">
128 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.abund\.list" format="mothur.list"/>
129 <filter>search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
130 </collection>
131 <collection name="rare_list_coll" type="list" label="${tool.name} on ${on_string}: rare.list">
132 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rare\.list" format="mothur.list"/>
133 <filter>search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
134 </collection>
135 <collection name="abund_accnos_coll" type="list" label="${tool.name} on ${on_string}: abund.accnos">
136 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.abund\.accnos" format="mothur.accnos"/>
137 <filter>(search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes')) and accnos</filter>
138 </collection>
139 <collection name="rare_accnos_coll" type="list" label="${tool.name} on ${on_string}: rare.accnos">
140 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rare\.accnos" format="mothur.accnos"/>
141 <filter>(search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes')) and accnos</filter>
142 </collection>
143 <collection name="abund_groups_coll" type="list" label="${tool.name} on ${on_string}: abund.groups">
144 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.abund\.groups" format="mothur.groups"/>
145 <filter>search['type'] != 'count' and split['dosplit'] == 'yes'</filter>
146 </collection>
147 <collection name="rare_groups_coll" type="list" label="${tool.name} on ${on_string}: rare.groups">
148 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rare\.groups" format="mothur.groups"/>
149 <filter>search['type'] != 'count' and split['dosplit'] == 'yes'</filter>
150 </collection>
151 <collection name="abund_names_coll" type="list" label="${tool.name} on ${on_string}: abund.names">
152 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.abund\.names" format="mothur.names"/>
153 <filter>search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
154 </collection>
155 <collection name="rare_names_coll" type="list" label="${tool.name} on ${on_string}: rare.names">
156 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rare\.names" format="mothur.names"/>
157 <filter>search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
158 </collection>
159 </outputs>
160 <tests>
161 <test><!-- test with count table -->
162 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
163 <param name="type" value="count"/>
164 <param name="input" value="amazon.count_table" ftype="mothur.count_table"/>
165 <param name="cutoff" value="1"/>
166 <param name="accnos" value="true"/>
167 <output name="abund_fasta" md5="3c147ce7224bc8c8602d2ccfe4b6eae7" ftype="fasta"/>
168 <output name="rare_fasta" md5="bff57d4585fe4e6d8b86c949f3e17e1a" ftype="fasta"/>
169 <output name="abund_count" md5="288e5222f3d454b67761fca3c8c944b1" ftype="mothur.count_table"/>
170 <output name="rare_count" md5="dc7be856861ef53faa73a5312b0661c3" ftype="mothur.count_table"/>
171 <output name="abund_accnos" md5="47c918c965d41fea12bad748afe60833" ftype="mothur.accnos"/>
172 <output name="rare_accnos" md5="3537f34f96d276e72e03f6d6a4994fd9" ftype="mothur.accnos"/>
173 <expand macro="logfile-test"/>
174 </test>
175 <test><!-- test with name file and accnos output -->
176 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
177 <param name="type" value="name"/>
178 <param name="input" value="amazon.names" ftype="mothur.names"/>
179 <param name="cutoff" value="1"/>
180 <param name="accnos" value="true"/>
181 <output name="abund_fasta" md5="3c147ce7224bc8c8602d2ccfe4b6eae7" ftype="fasta"/>
182 <output name="rare_fasta" md5="bff57d4585fe4e6d8b86c949f3e17e1a" ftype="fasta"/>
183 <output name="abund_names" md5="41560e422d53c83cb482ef868409136c" ftype="mothur.names"/>
184 <output name="rare_names" md5="12527477b2c1891c9278f417a5ece45d" ftype="mothur.names"/>
185 <output name="abund_accnos" md5="47c918c965d41fea12bad748afe60833" ftype="mothur.accnos"/>
186 <output name="rare_accnos" md5="3537f34f96d276e72e03f6d6a4994fd9" ftype="mothur.accnos"/>
187 <expand macro="logfile-test"/>
188 </test>
189 <test><!-- test with name file and accnos output with groups-->
190 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
191 <param name="type" value="name"/>
192 <param name="input" value="amazon.names" ftype="mothur.names"/>
193 <param name="cutoff" value="1"/>
194 <param name="accnos" value="true"/>
195 <param name="dosplit" value="yes"/>
196 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
197 <param name="groups" value="forest,pasture"/>
198 <output_collection name="abund_fasta_coll" count="2">
199 <element name="forest" md5="8d90da3c099450e31de006548e8f458c" ftype="fasta"/>
200 </output_collection>
201 <output_collection name="rare_fasta_coll" count="2">
202 <element name="forest" md5="4459f7ee4c46ccf0ce33f5694ac1ca49" ftype="fasta"/>
203 </output_collection>
204 <output_collection name="abund_names_coll" count="2">
205 <element name="pasture" md5="d45b69987a0294c87fab358bbb71cd29" ftype="mothur.names"/>
206 </output_collection>
207 <output_collection name="rare_names_coll" count="2">
208 <element name="pasture" md5="fc5d939ceca270be00b39d5323c1a79f" ftype="mothur.names"/>
209 </output_collection>
210 <output_collection name="abund_accnos_coll" count="2">
211 <element name="forest" md5="597a2cc6d2da897434ec9d2c11489d0a" ftype="mothur.accnos"/>
212 </output_collection>
213 <output_collection name="rare_accnos_coll" count="2">
214 <element name="forest" md5="20f8e54d68bf225f405258942e0cb5ac" ftype="mothur.accnos"/>
215 </output_collection>
216 <output_collection name="abund_groups_coll" count="2">
217 <element name="pasture" md5="46ac8394df6b3376b41619b07720ee18" ftype="mothur.groups"/>
218 </output_collection>
219 <output_collection name="rare_groups_coll" count="2">
220 <element name="pasture" md5="5907bd7fe874a29fcc57930ecb0f65d1" ftype="mothur.groups"/>
221 </output_collection>
222 <expand macro="logfile-test"/>
223 </test>
224 <test><!-- test with list -->
225 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
226 <param name="type" value="list"/>
227 <param name="input" value="amazon.an.list" ftype="mothur.list"/>
228 <param name="cutoff" value="2"/>
229 <param name="accnos" value="true"/>
230 <param name="dosplit" value="yes"/>
231 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
232 <param name="groups" value="forest,pasture"/>
233 <output_collection name="abund_fasta_coll" count="72">
234 <element name="0.05.forest" md5="1860c0cf143a2b7adc93c88418ed3559" ftype="fasta"/>
235 </output_collection>
236 <output_collection name="rare_fasta_coll" count="72">
237 <element name="0.05.pasture" md5="7c9ca6c2f3e2eb5c3d38c30963b3d976" ftype="fasta"/>
238 </output_collection>
239 <output_collection name="abund_list_coll" count="72">
240 <element name="forest.0.05" md5="8a0843911399171a73afbc0374065fd0" ftype="mothur.list"/>
241 </output_collection>
242 <output_collection name="rare_list_coll" count="72">
243 <element name="pasture.0.05" md5="b7dc64a835d318852dbadc0c3379d0bb" ftype="mothur.list"/>
244 </output_collection>
245 <output_collection name="abund_accnos_coll" count="72">
246 <element name="0.05.forest" md5="e9f9b640ca00c11cba5420069c916b12" ftype="mothur.accnos"/>
247 </output_collection>
248 <output_collection name="rare_accnos_coll" count="72">
249 <element name="0.05.pasture" md5="e866c488171950bb38e7ba4c8f2982c1" ftype="mothur.accnos"/>
250 </output_collection>
251 <output_collection name="abund_groups_coll" count="72">
252 <element name="0.05.forest" md5="fd404451b15195cadb637751a463a077" ftype="mothur.groups"/>
253 </output_collection>
254 <output_collection name="rare_groups_coll" count="72">
255 <element name="0.05.pasture" md5="ddcf8bc26a0815fd366deceec64133ee" ftype="mothur.groups"/>
256 </output_collection>
257 <expand macro="logfile-test"/>
258 </test>
259 <test><!-- test with list and label and group select-->
260 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
261 <param name="type" value="list"/>
262 <param name="input" value="amazon.an.list" ftype="mothur.list"/>
263 <param name="cutoff" value="2"/>
264 <param name="label" value="0.05,0.22"/>
265 <param name="accnos" value="true"/>
266 <param name="dosplit" value="yes"/>
267 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
268 <param name="groups" value="forest,pasture"/>
269 <output_collection name="abund_fasta_coll" count="4">
270 <element name="0.05.pasture" md5="51327cbf0c66c9c3074ca3456b021ead" ftype="fasta"/>
271 </output_collection>
272 <output_collection name="rare_fasta_coll" count="4">
273 <element name="0.05.pasture" md5="7c9ca6c2f3e2eb5c3d38c30963b3d976" ftype="fasta"/>
274 </output_collection>
275 <output_collection name="abund_list_coll" count="4">
276 <element name="forest.0.05" md5="8a0843911399171a73afbc0374065fd0" ftype="mothur.list"/>
277 </output_collection>
278 <output_collection name="rare_list_coll" count="4">
279 <element name="forest.0.05" md5="f79b02e37dbd7a7f76a60c269571396f" ftype="mothur.list"/>
280 </output_collection>
281 <output_collection name="abund_accnos_coll" count="4">
282 <element name="0.05.pasture" md5="3a875836ffebfeb037cd761ea1d0607e" ftype="mothur.accnos"/>
283 </output_collection>
284 <output_collection name="rare_accnos_coll" count="4">
285 <element name="0.05.pasture" md5="e866c488171950bb38e7ba4c8f2982c1" ftype="mothur.accnos"/>
286 </output_collection>
287 <output_collection name="abund_groups_coll" count="4">
288 <element name="0.05.forest" md5="fd404451b15195cadb637751a463a077" ftype="mothur.groups"/>
289 </output_collection>
290 <output_collection name="rare_groups_coll" count="4">
291 <element name="0.05.forest" md5="53a2f24a4d69f92661b94bc4b813ce69" ftype="mothur.groups"/>
292 </output_collection>
293 <expand macro="logfile-test"/>
294 </test>
295 </tests>
296 <help>
297 <![CDATA[
298
299 @MOTHUR_OVERVIEW@
300
301 **Command Documentation**
302
303 The split.abund_ command reads a fasta file and a list_ or a name_ file and splits the sequences into rare and abundant groups.
304
305 .. _list: https://www.mothur.org/wiki/List_file
306 .. _name: https://www.mothur.org/wiki/Name_file
307 .. _split.abund: https://www.mothur.org/wiki/Split.abund
308 ]]>
309 </help>
310 <expand macro="citations"/>
311 </tool>