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comparison dereplication.xml @ 0:fae6527990af draft

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Imported from capsule None
author iuc
date Thu, 21 May 2015 03:58:09 -0400
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children 8c4e2933a17a
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-1:000000000000 0:fae6527990af
1 <tool id="vsearch_dereplication" name="VSearch dereplication" version="@VERSION@.0">
2 <description></description>
3 <macros>
4 <import>vsearch_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <expand macro="version_command" />
9 <command>
10 <![CDATA[
11 vsearch
12 @GENERAL@
13 --derep_fulllength $infile
14 #if $maxuniquesize:
15 --maxuniquesize $maxuniquesize
16 #end if
17 #if $minuniquesize:
18 --minuniquesize $minuniquesize
19 #end if
20 --output $outfile
21 #if $sizein:
22 --sizein $sizein
23 #end if
24 #if $sizeout:
25 --sizeout $sizeout
26 #end if
27 --strand $strand
28 --topn $topn
29 #if $uc:
30 --uc $uc
31 #end if
32 ]]>
33 </command>
34 <inputs>
35 <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--derep_fulllength)" />
36 <expand macro="topn" />
37 <expand macro="sizein" />
38 <expand macro="sizeout" />
39 <expand macro="strand" />
40 <expand macro="uclust_like_output" />
41 <param name="minuniquesize" type="integer" value="" optional="True" label="Minimum abundance"
42 help="(--minuniquesize)"/>
43 <param name="maxuniquesize" type="integer" value="" optional="True" label="Maximum abundance"
44 help="(--maxuniquesize)"/>
45 </inputs>
46 <outputs>
47 <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
48 <data name="uc" format="fasta" label="${tool.name} on ${on_string}: UCLUST like output">
49 <filter>uc is True</filter>
50 </data>
51 </outputs>
52 <tests>
53 <test>
54 <param name="infile" value="AF091148_first_rep.fsa.bz2" ftype="fasta" />
55 <param name="strand" value="both" />
56 <param name="minuniquesize" value="1" />
57 <param name="maxuniquesize" value="100000" />
58 <param name="sizeout" value="--sizeout"/>
59 <param name="topn" value="10000" />
60 <output name="outfile" file="dereplication_result1.fasta" ftype="fasta" />
61 </test>
62 </tests>
63 <help>
64 <![CDATA[
65 **What it does**
66
67 Merge strictly identical sequences contained in filename. Identical sequences are
68 defined as having the same length and the same string of nucleotides (case insensitive,
69 T and U are considered the same).
70
71 Dereplication options
72 --derep_fulllength FILENAME dereplicate sequences in the given FASTA file
73 --maxuniquesize INT maximum abundance for output from dereplication
74 --minuniquesize INT minimum abundance for output from dereplication
75 --output FILENAME output FASTA file
76 --sizein read abundance annotation from input
77 --sizeout write abundance annotation to output
78 --strand dereplicate "plus" or "both" strands (plus)
79 --topn INT output just the n most abundant sequences
80 --uc FILENAME filename for UCLUST-like output
81
82
83 @EXTERNAL_DOCUMENTATION@
84
85 -------
86
87 @REFERENCES@
88
89
90 ]]>
91 </help>
92 <expand macro="citations" />
93 </tool>