Mercurial > repos > iuc > mothur_split_abund

comparison split.abund.xml @ 2:407a5352f0ec 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 22:01:54 -0400
parents b15d9a2d2311
children
comparison
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1:ede016062913 2:407a5352f0ec
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 "$fasta" fasta.dat && 13 ln -s '$fasta' fasta.dat &&
14 ln -s "$search.input" search_input.dat && 14 ln -s '$search.input' search_input.dat &&
15 #if $split.dosplit == "yes": 15 #if $split.dosplit == "yes":
16 ln -s "$split.group" split_group.dat && 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(",","-") },
17 #end if 25 #end if
18 26 #elif $search.type == "name":
19 echo 'split.abund( 27 name=search_input.dat,
20 fasta=fasta.dat, 28 #else
21 #if $search.type == "list": 29 count=search_input.dat,
22 list=search_input.dat, 30 #end if
23 #if $search.label: 31 #if $split.dosplit == "yes":
24 label=${ str($search.label).replace(",","-") }, 32 #if $split.group:
25 #end if 33 group=split_group.dat,
26 #elif $search.type == "name": 34 #end if
27 name=search_input.dat, 35 #if $split.groups:
28 #else 36 groups=${ str($split.groups).replace(",","-") },
29 count=search_input.dat, 37 #end if
30 #end if 38 #end if
31 #if $split.dosplit == "yes": 39 accnos=$accnos,
32 #if $split.group: 40 cutoff=$cutoff
33 group=split_group.dat, 41 )'
34 #end if 42 | sed 's/ //g' ## mothur trips over whitespace
35 #if $split.groups: 43 | mothur
36 groups=${ str($split.groups).replace(",","-") }, 44 | tee mothur.out.log
37 #end if
38 #end if
39 accnos=$accnos,
40 cutoff=$cutoff
41 )'
42 | sed 's/ //g' ## mothur trips over whitespace
43 | mothur
44 | tee mothur.out.log
45 ]]></command> 45 ]]></command>
46 <inputs> 46 <inputs>
47 <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/> 47 <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
48 <param name="cutoff" type="integer" value="10" min="0" label="cutoff - Cutoff parameter is used to qualify what is abundant and rare."/> 48 <param name="cutoff" type="integer" value="10" min="0" label="cutoff - Cutoff parameter is used to qualify what is abundant and rare."/>
49 <conditional name="search"> 49 <conditional name="search">
81 </param> 81 </param>
82 </when> 82 </when>
83 <when value="no"/> 83 <when value="no"/>
84 </conditional> 84 </conditional>
85 <param name="accnos" type="boolean" truevalue="true" falsevalue="false" checked="false" label="accnos - Produce rare and abundant Accession outputs"/> 85 <param name="accnos" type="boolean" truevalue="true" falsevalue="false" checked="false" label="accnos - Produce rare and abundant Accession outputs"/>
86 <expand macro="param-savelog"/>
86 </inputs> 87 </inputs>
87 <outputs> 88 <outputs>
88 <expand macro="logfile-output"/> 89 <expand macro="logfile-output"/>
89 <data name="abund_fasta" format_source="fasta" from_work_dir="*abund.fasta" label="${tool.name} on ${on_string}: abund.fasta"> 90 <data name="abund_fasta" format_source="fasta" from_work_dir="*abund.fasta" label="${tool.name} on ${on_string}: abund.fasta">
90 <filter>search['type'] != 'list'</filter> 91 <filter>search['type'] != 'list'</filter>
168 <output name="rare_fasta" md5="bff57d4585fe4e6d8b86c949f3e17e1a" ftype="fasta"/> 169 <output name="rare_fasta" md5="bff57d4585fe4e6d8b86c949f3e17e1a" ftype="fasta"/>
169 <output name="abund_count" md5="288e5222f3d454b67761fca3c8c944b1" ftype="mothur.count_table"/> 170 <output name="abund_count" md5="288e5222f3d454b67761fca3c8c944b1" ftype="mothur.count_table"/>
170 <output name="rare_count" md5="dc7be856861ef53faa73a5312b0661c3" ftype="mothur.count_table"/> 171 <output name="rare_count" md5="dc7be856861ef53faa73a5312b0661c3" ftype="mothur.count_table"/>
171 <output name="abund_accnos" md5="47c918c965d41fea12bad748afe60833" ftype="mothur.accnos"/> 172 <output name="abund_accnos" md5="47c918c965d41fea12bad748afe60833" ftype="mothur.accnos"/>
172 <output name="rare_accnos" md5="3537f34f96d276e72e03f6d6a4994fd9" ftype="mothur.accnos"/> 173 <output name="rare_accnos" md5="3537f34f96d276e72e03f6d6a4994fd9" ftype="mothur.accnos"/>
174 <param name="savelog" value="true"/>
173 <expand macro="logfile-test"/> 175 <expand macro="logfile-test"/>
174 </test> 176 </test>
175 <test><!-- test with name file and accnos output --> 177 <test><!-- test with name file and accnos output -->
176 <param name="fasta" value="amazon.fasta" ftype="fasta"/> 178 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
177 <param name="type" value="name"/> 179 <param name="type" value="name"/>
182 <output name="rare_fasta" md5="bff57d4585fe4e6d8b86c949f3e17e1a" ftype="fasta"/> 184 <output name="rare_fasta" md5="bff57d4585fe4e6d8b86c949f3e17e1a" ftype="fasta"/>
183 <output name="abund_names" md5="41560e422d53c83cb482ef868409136c" ftype="mothur.names"/> 185 <output name="abund_names" md5="41560e422d53c83cb482ef868409136c" ftype="mothur.names"/>
184 <output name="rare_names" md5="12527477b2c1891c9278f417a5ece45d" ftype="mothur.names"/> 186 <output name="rare_names" md5="12527477b2c1891c9278f417a5ece45d" ftype="mothur.names"/>
185 <output name="abund_accnos" md5="47c918c965d41fea12bad748afe60833" ftype="mothur.accnos"/> 187 <output name="abund_accnos" md5="47c918c965d41fea12bad748afe60833" ftype="mothur.accnos"/>
186 <output name="rare_accnos" md5="3537f34f96d276e72e03f6d6a4994fd9" ftype="mothur.accnos"/> 188 <output name="rare_accnos" md5="3537f34f96d276e72e03f6d6a4994fd9" ftype="mothur.accnos"/>
189 <param name="savelog" value="true"/>
187 <expand macro="logfile-test"/> 190 <expand macro="logfile-test"/>
188 </test> 191 </test>
189 <test><!-- test with name file and accnos output with groups--> 192 <test><!-- test with name file and accnos output with groups-->
190 <param name="fasta" value="amazon.fasta" ftype="fasta"/> 193 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
191 <param name="type" value="name"/> 194 <param name="type" value="name"/>
217 <element name="pasture" md5="46ac8394df6b3376b41619b07720ee18" ftype="mothur.groups"/> 220 <element name="pasture" md5="46ac8394df6b3376b41619b07720ee18" ftype="mothur.groups"/>
218 </output_collection> 221 </output_collection>
219 <output_collection name="rare_groups_coll" count="2"> 222 <output_collection name="rare_groups_coll" count="2">
220 <element name="pasture" md5="5907bd7fe874a29fcc57930ecb0f65d1" ftype="mothur.groups"/> 223 <element name="pasture" md5="5907bd7fe874a29fcc57930ecb0f65d1" ftype="mothur.groups"/>
221 </output_collection> 224 </output_collection>
225 <param name="savelog" value="true"/>
222 <expand macro="logfile-test"/> 226 <expand macro="logfile-test"/>
223 </test> 227 </test>
224 <test><!-- test with list --> 228 <test><!-- test with list -->
225 <param name="fasta" value="amazon.fasta" ftype="fasta"/> 229 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
226 <param name="type" value="list"/> 230 <param name="type" value="list"/>
252 <element name="0.05.forest" md5="fd404451b15195cadb637751a463a077" ftype="mothur.groups"/> 256 <element name="0.05.forest" md5="fd404451b15195cadb637751a463a077" ftype="mothur.groups"/>
253 </output_collection> 257 </output_collection>
254 <output_collection name="rare_groups_coll" count="72"> 258 <output_collection name="rare_groups_coll" count="72">
255 <element name="0.05.pasture" md5="ddcf8bc26a0815fd366deceec64133ee" ftype="mothur.groups"/> 259 <element name="0.05.pasture" md5="ddcf8bc26a0815fd366deceec64133ee" ftype="mothur.groups"/>
256 </output_collection> 260 </output_collection>
261 <param name="savelog" value="true"/>
257 <expand macro="logfile-test"/> 262 <expand macro="logfile-test"/>
258 </test> 263 </test>
259 <test><!-- test with list and label and group select--> 264 <test><!-- test with list and label and group select-->
260 <param name="fasta" value="amazon.fasta" ftype="fasta"/> 265 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
261 <param name="type" value="list"/> 266 <param name="type" value="list"/>
288 <element name="0.05.forest" md5="fd404451b15195cadb637751a463a077" ftype="mothur.groups"/> 293 <element name="0.05.forest" md5="fd404451b15195cadb637751a463a077" ftype="mothur.groups"/>
289 </output_collection> 294 </output_collection>
290 <output_collection name="rare_groups_coll" count="4"> 295 <output_collection name="rare_groups_coll" count="4">
291 <element name="0.05.forest" md5="53a2f24a4d69f92661b94bc4b813ce69" ftype="mothur.groups"/> 296 <element name="0.05.forest" md5="53a2f24a4d69f92661b94bc4b813ce69" ftype="mothur.groups"/>
292 </output_collection> 297 </output_collection>
298 <param name="savelog" value="true"/>
293 <expand macro="logfile-test"/> 299 <expand macro="logfile-test"/>
294 </test> 300 </test>
295 </tests> 301 </tests>
296 <help> 302 <help><![CDATA[
297 <![CDATA[
298 303
299 @MOTHUR_OVERVIEW@ 304 @MOTHUR_OVERVIEW@
300 305
301 **Command Documentation** 306 **Command Documentation**
302 307
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. 308 The split.abund_ command reads a fasta file and a list_ or a name_ file and splits the sequences into rare and abundant groups.
304 309
305 .. _list: https://www.mothur.org/wiki/List_file 310 .. _list: https://www.mothur.org/wiki/List_file
306 .. _name: https://www.mothur.org/wiki/Name_file 311 .. _name: https://www.mothur.org/wiki/Name_file
307 .. _split.abund: https://www.mothur.org/wiki/Split.abund 312 .. _split.abund: https://www.mothur.org/wiki/Split.abund
308 ]]> 313
309 </help> 314 ]]></help>
310 <expand macro="citations"/> 315 <expand macro="citations"/>
311 </tool> 316 </tool>