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comparison clustering.xml @ 5:e8401372796a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 78d01e165304e0be6e6fd017b7314465492d7542
author iuc
date Thu, 17 Dec 2015 12:51:04 -0500
parents eb4910c5de12
children 50cc0d99b800
comparison
equal deleted inserted replaced
4:eb4910c5de12 5:e8401372796a
1 <tool id="vsearch_clustering" name="VSearch clustering" version="@VERSION@.1"> 1 <tool id="vsearch_clustering" name="VSearch clustering" version="@VERSION@.2">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>vsearch_macros.xml</import> 4 <import>vsearch_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
9 <command> 9 <command>
10 <![CDATA[ 10 <![CDATA[
11 vsearch 11 vsearch
12 @GENERAL@ 12 @GENERAL@
13 13
14 #if $clustering_mode.clustering_mode_select == 'cluster_fast': 14 #if $clustering_mode.clustering_mode_select == 'cluster_fast':
15 --cluster_fast "$infile" 15 --cluster_fast "$infile"
16 #else if $clustering_mode.clustering_mode_select == 'cluster_smallmem': 16 #else if $clustering_mode.clustering_mode_select == 'cluster_smallmem':
17 --cluster_smallmem "$infile" 17 --cluster_smallmem "$infile"
18 #end if 18 #end if
19 ##--clusters STRING output each cluster to a separate FASTA file 19 ##--clusters STRING output each cluster to a separate FASTA file
20 20
21 #if $maxrejects: 21 #if $maxrejects:
22 --maxrejects $maxrejects 22 --maxrejects "$maxrejects"
23 #end if 23 #end if
24 #if $maxaccepts: 24 #if $maxaccepts:
25 --maxaccepts $maxaccepts 25 --maxaccepts "$maxaccepts"
26 #end if 26 #end if
27 27
28 $cons_truncate 28 $cons_truncate
29 --id $id 29 --id "$id"
30 --iddef $iddef 30 --iddef "$iddef"
31 31
32 #if '--msaout' in str($outputs): 32 #if '--msaout' in str($outputs).split( "," ):
33 --msaout $msaout 33 --msaout "$msaout"
34 #end if 34 #end if
35 #if '--consout' in str($outputs): 35 #if '--consout' in str($outputs).split( "," ):
36 --consout $consout 36 --consout "$consout"
37 #end if 37 #end if
38 #if '--centroids' in str($outputs): 38 #if '--centroids' in str($outputs).split( "," ):
39 --centroids $centroids 39 --centroids "$centroids"
40 #end if 40 #end if
41 #if '--alnout' in str($outputs): 41 #if '--alnout' in str($outputs).split( "," ):
42 --alnout $alnout 42 --alnout "$alnout"
43 #end if 43 #end if
44 #if '--blast6out' in str($outputs): 44 #if '--blast6out' in str($outputs).split( "," ):
45 --blast6out $blast6out 45 --blast6out "$blast6out"
46 #end if 46 #end if
47 #if '--notmatched' in str($outputs): 47 #if '--notmatched' in str($outputs).split( "," ):
48 --notmatched $notmatched 48 --notmatched "$notmatched"
49 #end if 49 #end if
50 #if '--fastapairs' in str($outputs): 50 #if '--fastapairs' in str($outputs).split( "," ):
51 --fastapairs $fastapairs 51 --fastapairs "$fastapairs"
52 #end if 52 #end if
53 #if '--matched' in str($outputs): 53 #if '--matched' in str($outputs).split( "," ):
54 --matched $matched 54 --matched "$matched"
55 #end if 55 #end if
56 #if $qmask != 'no': 56 #if str( $qmask ) != 'no':
57 --qmask $qmask 57 --qmask "$qmask"
58 #end if 58 #end if
59 $sizein 59 $sizein
60 $sizeout 60 $sizeout
61 --strand $strand 61 --strand "$strand"
62 $usersort 62 $usersort
63 #if $uc: 63 #if $uc:
64 --uc "$uc_outfile" 64 --uc "$uc_outfile"
65 #end if 65 #end if
66 66
223 --usersort indicate sequences not presorted by length 223 --usersort indicate sequences not presorted by length
224 224
225 225
226 @EXTERNAL_DOCUMENTATION@ 226 @EXTERNAL_DOCUMENTATION@
227 227
228 -------
229
230 @REFERENCES@
231
232 228
233 ]]> 229 ]]>
234 </help> 230 </help>
235 <expand macro="citations" /> 231 <expand macro="citations" />
236 </tool> 232 </tool>