Mercurial > repos > iuc > mothur_split_abund

comparison split.abund.xml @ 3:ef779f6cb288 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:22:51 -0500
parents 59ab81a8d28d
children 607eee4176b0
comparison
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2:e2ce9529fc1d 3:ef779f6cb288
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">
291 <element name="0.05.forest" md5="53a2f24a4d69f92661b94bc4b813ce69" ftype="mothur.groups"/> 291 <element name="0.05.forest" md5="53a2f24a4d69f92661b94bc4b813ce69" ftype="mothur.groups"/>
292 </output_collection> 292 </output_collection>
293 <expand macro="logfile-test"/> 293 <expand macro="logfile-test"/>
294 </test> 294 </test>
295 </tests> 295 </tests>
296 <help> 296 <help><![CDATA[
297 <![CDATA[
298 297
299 @MOTHUR_OVERVIEW@ 298 @MOTHUR_OVERVIEW@
300 299
301 **Command Documentation** 300 **Command Documentation**
302 301
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. 302 The split.abund_ command reads a fasta file and a list_ or a name_ file and splits the sequences into rare and abundant groups.
304 303
305 .. _list: https://www.mothur.org/wiki/List_file 304 .. _list: https://www.mothur.org/wiki/List_file
306 .. _name: https://www.mothur.org/wiki/Name_file 305 .. _name: https://www.mothur.org/wiki/Name_file
307 .. _split.abund: https://www.mothur.org/wiki/Split.abund 306 .. _split.abund: https://www.mothur.org/wiki/Split.abund
308 ]]> 307
309 </help> 308 ]]></help>
310 <expand macro="citations"/> 309 <expand macro="citations"/>
311 </tool> 310 </tool>