Mercurial > repos > iuc > mothur_get_communitytype

comparison get.communitytype.xml @ 2:38def0f0b7cc 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 09:15:33 -0500
parents c927518943fc
children 6d432db714ed
comparison
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1:eb98c05f5cee 2:38def0f0b7cc
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 '$otu' shared.dat && 13 ln -s '$otu' shared.dat &&
14 14
15 echo 'get.communitytype( 15 echo 'get.communitytype(
16 shared=shared.dat, 16 shared=shared.dat,
17 #if $label: 17 #if $label:
18 label=${ str($label).replace(",","-") }, 18 label=${ str($label).replace(",","-") },
19 #end if 19 #end if
20 #if $groups: 20 #if $groups:
21 groups=${ str($groups).replace(",","-") }, 21 groups=${ str($groups).replace(",","-") },
22 #end if 22 #end if
23 method=$m.method, 23 method=$m.method,
24 #if $m.method == 'kmeans' or $m.method == 'pams': 24 #if $m.method == 'kmeans' or $m.method == 'pams':
25 calc=$m.calc, 25 calc=$m.calc,
26 iters=$m.iters, 26 iters=$m.iters,
27 #end if 27 #end if
28 #if int($subsample) == 0: 28 #if int($subsample) == 0:
29 subsample=T, 29 subsample=T,
30 #elif int($subsample) > 0: 30 #elif int($subsample) > 0:
31 subsample=$subsample, 31 subsample=$subsample,
32 #end if 32 #end if
33 minpartitions=$minpartitions, 33 minpartitions=$minpartitions,
34 maxpartitions=$maxpartitions, 34 maxpartitions=$maxpartitions,
35 optimizegap=$optimizegap, 35 optimizegap=$optimizegap,
36 processors='\${GALAXY_SLOTS:-8}' 36 processors='\${GALAXY_SLOTS:-8}'
37 )' 37 )'
38 | sed 's/ //g' ## mothur trips over whitespace 38 | sed 's/ //g' ## mothur trips over whitespace
39 | mothur 39 | mothur
40 | tee mothur.out.log 40 | tee mothur.out.log
41 ]]></command> 41 ]]></command>
42 <inputs> 42 <inputs>
43 <param name="otu" type="data" format="mothur.shared" label="shared - Shared file"/> 43 <param name="otu" type="data" format="mothur.shared" label="shared - Shared file"/>
44 <param name="label" type="select" label="label - OTU Labels" multiple="true" optional="true"> 44 <param name="label" type="select" label="label - OTU Labels" multiple="true" optional="true">
45 <expand macro="labeloptions"/> 45 <expand macro="labeloptions"/>