Mercurial > repos > iuc > vsearch
comparison clustering.xml @ 2:f29e21388219 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
author | iuc |
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date | Thu, 17 Dec 2015 12:53:39 -0500 |
parents | 8c4e2933a17a |
children | 4258854759ba |
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1:8c4e2933a17a | 2:f29e21388219 |
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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> |