annotate clustering.xml @ 6:9495df9dd6ef draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb"
author iuc
date Wed, 04 Nov 2020 07:36:19 +0000
parents 576963db5f1b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
4258854759ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 29f6e6424a37947adbe1eba92f0e7d3c83efc042-dirty
iuc
parents: 2
diff changeset
1 <tool id="vsearch_clustering" name="VSearch clustering" version="@VERSION@.0">
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
2 <description></description>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
3 <macros>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
4 <import>vsearch_macros.xml</import>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
5 </macros>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
6 <expand macro="requirements" />
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
7 <expand macro="stdio" />
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
8 <expand macro="version_command" />
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
9 <command>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
10 <![CDATA[
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
11 vsearch
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
12 @GENERAL@
3
4258854759ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 29f6e6424a37947adbe1eba92f0e7d3c83efc042-dirty
iuc
parents: 2
diff changeset
13
4258854759ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 29f6e6424a37947adbe1eba92f0e7d3c83efc042-dirty
iuc
parents: 2
diff changeset
14 #if $clustering_mode.clustering_mode_select == 'cluster_fast':
1
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
15 --cluster_fast "$infile"
3
4258854759ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 29f6e6424a37947adbe1eba92f0e7d3c83efc042-dirty
iuc
parents: 2
diff changeset
16 #else if $clustering_mode.clustering_mode_select == 'cluster_smallmem':
1
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
17 --cluster_smallmem "$infile"
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
18 #end if
3
4258854759ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 29f6e6424a37947adbe1eba92f0e7d3c83efc042-dirty
iuc
parents: 2
diff changeset
19 ##--clusters STRING output each cluster to a separate FASTA file
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
20
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
21 #if $maxrejects:
2
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
22 --maxrejects "$maxrejects"
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
23 #end if
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
24 #if $maxaccepts:
2
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
25 --maxaccepts "$maxaccepts"
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
26 #end if
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
27
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
28 $cons_truncate
2
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
29 --id "$id"
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
30 --iddef "$iddef"
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
31
2
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
32 #if '--msaout' in str($outputs).split( "," ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
33 --msaout "$msaout"
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
34 #end if
2
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
35 #if '--consout' in str($outputs).split( "," ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
36 --consout "$consout"
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
37 #end if
2
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
38 #if '--centroids' in str($outputs).split( "," ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
39 --centroids "$centroids"
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
40 #end if
2
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
41 #if '--alnout' in str($outputs).split( "," ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
42 --alnout "$alnout"
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
43 #end if
2
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
44 #if '--blast6out' in str($outputs).split( "," ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
45 --blast6out "$blast6out"
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
46 #end if
2
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
47 #if '--notmatched' in str($outputs).split( "," ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
48 --notmatched "$notmatched"
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
49 #end if
2
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
50 #if '--fastapairs' in str($outputs).split( "," ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
51 --fastapairs "$fastapairs"
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
52 #end if
2
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
53 #if '--matched' in str($outputs).split( "," ):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
54 --matched "$matched"
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
55 #end if
2
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
56 #if str( $qmask ) != 'no':
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
57 --qmask "$qmask"
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
58 #end if
1
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
59 $sizein
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
60 $sizeout
2
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
iuc
parents: 1
diff changeset
61 --strand "$strand"
3
4258854759ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 29f6e6424a37947adbe1eba92f0e7d3c83efc042-dirty
iuc
parents: 2
diff changeset
62 $usersort
4258854759ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 29f6e6424a37947adbe1eba92f0e7d3c83efc042-dirty
iuc
parents: 2
diff changeset
63 #if $uc:
1
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
64 --uc "$uc_outfile"
3
4258854759ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 29f6e6424a37947adbe1eba92f0e7d3c83efc042-dirty
iuc
parents: 2
diff changeset
65 #end if
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
66
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
67 ]]>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
68 </command>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
69 <inputs>
1
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
70 <param name="infile" type="data" format="fasta" label="Select your input FASTA file" help="" />
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
71 <conditional name="clustering_mode">
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
72 <param name="clustering_mode_select" type="select" label="Choose sorting method to use before clustering" help="">
4
576963db5f1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f
iuc
parents: 3
diff changeset
73 <option value="cluster_fast" selected="True">Cluster sequences after sorting by length (--cluster-fast)</option>
1
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
74 <option value="cluster_smallmem">Cluster already sorted sequences (--cluster-smallmem)</option>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
75 </param>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
76 <when value="cluster_fast">
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
77 </when>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
78 <when value="cluster_smallmem">
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
79 </when>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
80 </conditional>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
81 <param name="usersort" type="boolean" truevalue="--usersort" falsevalue="" checked="False"
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
82 label="Indicate that input sequences are not presorted by length" help="(--usersort)"/>
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
83 <expand macro="id_and_iddef" />
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
84 <param name="cons_truncate" type="boolean" truevalue="--cons_truncate" falsevalue="" checked="False"
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
85 label="Do not ignore terminal gaps in MSA for consensus" help="(--cons_truncate)"/>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
86 <expand macro="qmask" />
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
87 <expand macro="sizein" />
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
88 <expand macro="sizeout" />
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
89 <expand macro="strand" />
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
90 <expand macro="maxrejects" />
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
91 <expand macro="maxaccepts" />
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
92 <expand macro="general_output">
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
93 <option value="--msaout">Multiple sequence alignments</option>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
94 <option value="--consout">Cluster consensus sequences</option>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
95 <option value="--centroids">Centroid sequences</option>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
96 <option value="--notmatched">Write non-matching query sequences to separate file</option>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
97 <option value="--matched">Write matching query sequences to separate file</option>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
98 </expand>
1
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
99 <expand macro="uclust_like_output" />
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
100
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
101 </inputs>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
102 <outputs>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
103 <data name="msaout" format="fasta" label="${tool.name} on ${on_string}: Multiple Sequence Alignments">
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
104 <filter>'--msaout' in outputs</filter>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
105 </data>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
106 <data name="consout" format="fasta" label="${tool.name} on ${on_string}: Consensus Sequences">
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
107 <filter>'--consout' in outputs</filter>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
108 </data>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
109 <data name="centroids" format="fasta" label="${tool.name} on ${on_string}: Cluster centroids">
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
110 <filter>'--centroids' in outputs</filter>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
111 </data>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
112 <data name="alnout" format="fasta" label="${tool.name} on ${on_string}: Alignment">
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
113 <filter>'--alnout' in outputs</filter>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
114 </data>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
115 <data name="notmatched" format="fasta" label="${tool.name} on ${on_string}: Non-matched queries">
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
116 <filter>'--notmatched' in outputs</filter>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
117 </data>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
118 <data name="matched" format="fasta" label="${tool.name} on ${on_string}: Matching query sequences">
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
119 <filter>'--matched' in outputs</filter>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
120 </data>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
121 <data name="blast6out" format="tabular" label="${tool.name} on ${on_string}: BLAST like tabular">
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
122 <filter>'--blast6out' in outputs</filter>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
123 </data>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
124 <data name="fastapairs" format="fasta" label="${tool.name} on ${on_string}: Query/Target sequences">
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
125 <filter>'--fastapairs' in outputs</filter>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
126 </data>
1
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
127 <data name="uc_outfile" format="tabular" label="${tool.name} on ${on_string}: UCLUST like output">
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
128 <filter>uc is True</filter>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
129 </data>
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
130 </outputs>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
131 <tests>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
132 <test>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
133 <param name="infile" value="BioMarKs5k.fsa.bz2" ftype="fasta" />
1
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
134 <param name="clustering_mode_select" value="cluster_smallmem"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
135 <param name="usersort" value="--usersort"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
136 <param name="id" value="0.99"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
137 <param name="maxaccepts" value="1"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
138 <param name="maxrejects" value="2"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
139 <param name="sizeout" value="--sizeout"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
140 <param name="outputs" value="--centroids,--blast6out,--notmatched" />
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
141 <output name="centroids" file="clustering_centroids_result2.fasta" ftype="fasta" />
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
142 <output name="blast6out" file="clustering_blast6out_result2.tab" ftype="tabular" />
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
143 <output name="notmatched" file="clustering_notmatched_result2.fasta" ftype="fasta" />
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
144 </test>
3
4258854759ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 29f6e6424a37947adbe1eba92f0e7d3c83efc042-dirty
iuc
parents: 2
diff changeset
145 <test>
1
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
146 <param name="infile" value="BioMarKs5k.fsa.bz2" ftype="fasta" />
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
147 <param name="clustering_mode_select" value="cluster_smallmem"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
148 <param name="usersort" value="--usersort"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
149 <param name="id" value="0.99"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
150 <param name="maxaccepts" value="1"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
151 <param name="maxrejects" value="2"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
152 <param name="sizeout" value="--sizeout"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
153 <param name="outputs" value="--centroids" />
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
154 <param name="uc" value="--uc"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
155 <output name="centroids" file="clustering_centroids_result2.fasta" ftype="fasta" />
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
156 <output name="uc_outfile" file="clustering_uc_result3.uc" ftype="tabular" />
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
157 </test>
3
4258854759ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 29f6e6424a37947adbe1eba92f0e7d3c83efc042-dirty
iuc
parents: 2
diff changeset
158 <test>
1
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
159 <param name="infile" value="BioMarKs5k.fsa.bz2" ftype="fasta" />
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
160 <param name="clustering_mode_select" value="cluster_smallmem"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
161 <param name="usersort" value="--usersort"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
162 <param name="id" value="0.99"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
163 <param name="maxaccepts" value="1"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
164 <param name="maxrejects" value="2"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
165 <param name="sizeout" value="--sizeout"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
166 <param name="outputs" value="--centroids" />
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
167 <param name="iddef" value="0"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
168 <output name="centroids" file="clustering_centroids_result4.fasta" ftype="fasta" />
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
169 </test>
3
4258854759ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 29f6e6424a37947adbe1eba92f0e7d3c83efc042-dirty
iuc
parents: 2
diff changeset
170 <test>
1
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
171 <param name="infile" value="BioMarKs5k.fsa.bz2" ftype="fasta" />
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
172 <param name="clustering_mode_select" value="cluster_fast"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
173 <param name="usersort" value="--usersort"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
174 <param name="id" value="0.99"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
175 <param name="maxaccepts" value="1"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
176 <param name="maxrejects" value="2"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
177 <param name="sizeout" value=""/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
178 <param name="outputs" value="--centroids" />
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
179 <param name="qmask" value="none"/>
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
180 <output name="centroids" file="clustering_centroids_result1.fasta" ftype="fasta" />
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
181 </test>
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
182 </tests>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
183 <help>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
184 <![CDATA[
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
185 **What it does**
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
186
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
187 vsearch implements a single-pass, greedy star-clustering algorithm, similar to the algorithms
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
188 implemented in usearch, DNAclust and sumaclust for example.
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
189
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
190
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
191 Clustering options (most searching options also apply)
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
192 --centroids FILENAME output centroid sequences to FASTA file
1
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
193 --cluster_fast FILENAME cluster sequences after sorting by length
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
194 --cluster_size FILENAME cluster sequences after sorting by abundance
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
195 --cluster_smallmem FILENAME cluster already sorted sequences (see -usersort)
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
196 --clusters STRING output each cluster to a separate FASTA file
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
197 --consout FILENAME output cluster consensus sequences to FASTA file
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
198 --cons_truncate do not ignore terminal gaps in MSA for consensus
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
199 --id REAL reject if identity lower
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
200 --iddef INT id definition, 0-4=CD-HIT,all,int,MBL,BLAST (2)
1
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
201 --msaout FILENAME output multiple seq. alignments to FASTA file
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
202 --qmask seqs with dust, soft or no method (dust)
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
203 --sizein propagate abundance annotation from input
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
204 --sizeout write cluster abundances to centroid file
1
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
205 --strand cluster using plus or both strands (plus)
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
206 --uc FILENAME filename for UCLUST-like output
8c4e2933a17a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 95732e013ec4dfe5dae0b9ed81e9d7710cbaed9d
iuc
parents: 0
diff changeset
207 --usersort indicate sequences not presorted by length
0
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
208
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
209
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
210 @EXTERNAL_DOCUMENTATION@
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
211
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
212
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
213 ]]>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
214 </help>
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
215 <expand macro="citations" />
fae6527990af Imported from capsule None
iuc
parents:
diff changeset
216 </tool>