Mercurial > repos > iuc > vsearch

annotate dereplication.xml @ 2:90759bd72d2e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
author iuc
date Sun, 28 Jun 2015 22:49:34 -0400
parents 24e4f42410e5
children e8401372796a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
1 <tool id="vsearch_dereplication" name="VSearch dereplication" version="@VERSION@.1">
0
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
2 <description></description>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
3 <macros>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
4 <import>vsearch_macros.xml</import>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
5 </macros>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
6 <expand macro="requirements" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
7 <expand macro="stdio" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
8 <expand macro="version_command" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
9 <command>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
10 <![CDATA[
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
11 vsearch
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
12 @GENERAL@
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
13 --derep_fulllength $infile
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
14 #if $maxuniquesize:
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
15 --maxuniquesize $maxuniquesize
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
16 #end if
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
17 #if $minuniquesize:
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
18 --minuniquesize $minuniquesize
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
19 #end if
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
20 --output $outfile
2
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
21 $sizein
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
22 $sizeout
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
23 --strand $strand
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
24 #if $topn:
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
25 --topn $topn
0
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
26 #end if
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
27 #if $uc:
2
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
28 --uc $uc_outfile
0
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
29 #end if
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
30 ]]>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
31 </command>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
32 <inputs>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
33 <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--derep_fulllength)" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
34 <expand macro="topn" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
35 <expand macro="sizein" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
36 <expand macro="sizeout" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
37 <expand macro="strand" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
38 <expand macro="uclust_like_output" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
39 <param name="minuniquesize" type="integer" value="" optional="True" label="Minimum abundance"
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
40 help="(--minuniquesize)"/>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
41 <param name="maxuniquesize" type="integer" value="" optional="True" label="Maximum abundance"
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
42 help="(--maxuniquesize)"/>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
43 </inputs>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
44 <outputs>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
45 <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
2
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
46 <data name="uc_outfile" format="fasta" label="${tool.name} on ${on_string}: UCLUST like output">
0
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
47 <filter>uc is True</filter>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
48 </data>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
49 </outputs>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
50 <tests>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
51 <test>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
52 <param name="infile" value="AF091148_first_rep.fsa.bz2" ftype="fasta" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
53 <param name="strand" value="both" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
54 <param name="minuniquesize" value="1" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
55 <param name="maxuniquesize" value="100000" />
2
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
56 <param name="topn" value="10000" />
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
57 <output name="outfile" file="dereplication_result1.fasta" ftype="fasta" />
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
58 </test>
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
59 <test>
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
60 <param name="infile" value="AF091148_first_rep.fsa.bz2" ftype="fasta" />
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
61 <param name="strand" value="both" />
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
62 <param name="minuniquesize" value="1" />
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
63 <param name="maxuniquesize" value="100000" />
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
64 <param name="sizeout" value="--sizeout"/>
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
65 <param name="topn" value="" />
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
66 <output name="outfile" file="dereplication_result2.fasta" ftype="fasta" />
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
67 </test>
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
68 <test>
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
69 <param name="infile" value="AF091148_first_rep.fsa.bz2" ftype="fasta" />
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
70 <param name="strand" value="both" />
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
71 <param name="minuniquesize" value="1" />
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
72 <param name="maxuniquesize" value="100000" />
0
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
73 <param name="sizeout" value="--sizeout"/>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
74 <param name="topn" value="10000" />
2
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
75 <param name="uc" value="--uc" />
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
76 <output name="outfile" file="dereplication_result2.fasta" ftype="fasta" />
90759bd72d2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 968f7c9ef3e4db85d7cb2f6ab100ebc3200222e0
iuc
parents: 0
diff changeset
77 <output name="uc_outfile" file="dereplication_uc_result3.fasta" ftype="fasta" />
0
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
78 </test>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
79 </tests>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
80 <help>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
81 <![CDATA[
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
82 **What it does**
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
83
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
84 Merge strictly identical sequences contained in filename. Identical sequences are
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
85 defined as having the same length and the same string of nucleotides (case insensitive,
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
86 T and U are considered the same).
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
87
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
88 Dereplication options
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
89 --derep_fulllength FILENAME dereplicate sequences in the given FASTA file
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
90 --maxuniquesize INT maximum abundance for output from dereplication
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
91 --minuniquesize INT minimum abundance for output from dereplication
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
92 --output FILENAME output FASTA file
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
93 --sizein read abundance annotation from input
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
94 --sizeout write abundance annotation to output
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
95 --strand dereplicate "plus" or "both" strands (plus)
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
96 --topn INT output just the n most abundant sequences
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
97 --uc FILENAME filename for UCLUST-like output
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
98
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
99
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
100 @EXTERNAL_DOCUMENTATION@
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
101
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
102 -------
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
103
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
104 @REFERENCES@
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
105
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
106
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
107 ]]>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
108 </help>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
109 <expand macro="citations" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
parents:
diff changeset
110 </tool>