Mercurial > repos > iuc > abyss

annotate abyss-pe.xml @ 6:0e93176640ac 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/abyss commit b2a1b28e492c621204b836778d24d7b4d03a8823"
author iuc
date Mon, 13 Sep 2021 16:58:30 +0000
parents fa5259cc561b
children 841084c5fc46
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
0e93176640ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit b2a1b28e492c621204b836778d24d7b4d03a8823"
iuc
parents: 5
diff changeset
1 <tool id="abyss-pe" name="ABySS" version="@TOOL_VERSION@+galaxy0">
0
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
2 <description>de novo sequence assembler</description>
6
0e93176640ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit b2a1b28e492c621204b836778d24d7b4d03a8823"
iuc
parents: 5
diff changeset
3 <xrefs>
0e93176640ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit b2a1b28e492c621204b836778d24d7b4d03a8823"
iuc
parents: 5
diff changeset
4 <xref type="bio.tools">abyss</xref>
0e93176640ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit b2a1b28e492c621204b836778d24d7b4d03a8823"
iuc
parents: 5
diff changeset
5 </xrefs>
0
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
6 <macros>
6
0e93176640ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit b2a1b28e492c621204b836778d24d7b4d03a8823"
iuc
parents: 5
diff changeset
7 <token name="@TOOL_VERSION@">2.3.1</token>
0
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
8 <xml name="reads_conditional">
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
9 <conditional name="reads">
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
10 <param name="reads_selector" type="select" label="Type of paired-end datasets">
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
11 <option value="paired">2 separate datasets</option>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
12 <option value="paired_collection">1 paired dataset collection</option>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
13 <option value="paired_il">1 dataset of interleaved reads</option>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
14 </param>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
15 <when value="paired">
5
fa5259cc561b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 4
diff changeset
16 <param name="reads1" type="data" format="fasta,fastq,fastq.gz" label="Paired-end reads 1" />
fa5259cc561b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 4
diff changeset
17 <param name="reads2" type="data" format="fasta,fastq,fastq.gz" label="Paired-end reads 2" />
0
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
18 </when>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
19 <when value="paired_collection">
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
20 <param name="reads_coll" type="data_collection" collection_type="paired" format="fasta,fastq,fastqsanger,fastqillumina" label="Paired-end reads collection" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
21 </when>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
22 <when value="paired_il">
5
fa5259cc561b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 4
diff changeset
23 <param name="reads_il" type="data" format="fasta,fastq,fastq.gz" label="Interleaved paired-end reads" />
0
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
24 </when>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
25 </conditional>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
26 </xml>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
27 </macros>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
28 <requirements>
2
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
29 <requirement type="package" version="@TOOL_VERSION@">abyss</requirement>
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
30 <requirement type="package" version="0.7.17">bwa</requirement>
0
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
31 </requirements>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
32 <stdio>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
33 <!-- Anything other than zero is an error -->
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
34 <exit_code range="1:" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
35 <!-- In case the return code has not been set propery check stderr too -->
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
36 <regex match="Error:" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
37 <regex match="Exception:" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
38 </stdio>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
39 <version_command>ABYSS --version | head -n 1</version_command>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
40 <command>
2
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
41 abyss-pe
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
42 name=abyss
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
43 j=\${GALAXY_SLOTS:-1}
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
44 k=$k
1
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
parents: 0
diff changeset
45
2
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
46 #if str($K)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
47 K=$K
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
48 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
49 #if str($q)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
50 q=$q
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
51 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
52 #if str($Q)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
53 Q=$Q
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
54 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
55 #if str($e)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
56 e=$e
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
57 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
58 #if str($E)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
59 E=$E
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
60 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
61 #if str($t)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
62 t=$t
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
63 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
64 #if str($c)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
65 c=$c
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
66 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
67 #if str($b)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
68 b=$b
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
69 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
70 #if $SS
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
71 SS=--SS
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
72 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
73 #if str($m)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
74 m=$m
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
75 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
76 #if str($p)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
77 p=$p
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
78 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
79 #if str($a)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
80 a=$a
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
81 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
82 #if str($l)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
83 l=$l
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
84 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
85 #if str($s)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
86 s=$s
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
87 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
88 #if str($n)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
89 n=$n
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
90 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
91 #if str($d)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
92 d=$d
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
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93 #end if
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94 #if str($S)
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95 S=$S
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96 #end if
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97 #if str($N)
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98 N=$N
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99 #end if
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100 #if $lib_repeat
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101 lib='
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102 #for $i in range(len($lib_repeat))
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103 lib$i
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104 #end for
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105 '
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106 #for $i, $v in enumerate($lib_repeat)
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107 #if $v.reads.reads_selector == 'paired'
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108 lib${i}='${v.reads.reads1} ${v.reads.reads2}'
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109 #elif $v.reads.reads_selector == 'paired_collection'
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110 lib${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}'
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111 #else
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112 lib${i}='${v.reads.reads_il}'
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113 #end if
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114 #end for
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115 #end if
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116 #if str($se_reads) != 'None'
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117 se='
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118 #for $v in $se_reads
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119 $v
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120 #end for
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121 '
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122 #end if
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123 #if $mp_repeat
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124 mp='
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125 #for $i in range(len($mp_repeat))
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126 mp$i
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127 #end for
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128 '
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129 #for $i, $v in enumerate($mp_repeat)
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130 #if $v.reads.reads_selector == 'paired'
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131 mp${i}='${v.reads.reads1} ${v.reads.reads2}'
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132 #elif $v.reads.reads_selector == 'paired_collection'
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133 mp${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}'
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134 #else
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135 mp${i}='${v.reads.reads_il}'
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136 #end if
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137 #end for
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138 #end if
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139 #if str($long_seqs) != 'None'
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140 long='
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141 #for $i in range(len($long_seqs))
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142 long$i
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143 #end for
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144 '
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145 #for $i, $v in enumerate($long_seqs)
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146 long${i}='$v'
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147 #end for
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148 #end if
0
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149 </command>
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150
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151 <inputs>
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152 <repeat name="lib_repeat" title="Paired-end library" help="(lib)">
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153 <expand macro="reads_conditional" />
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154 </repeat>
5
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155 <param name="se_reads" argument="se" type="data" multiple="true" optional="true" format="fasta,fastq,fastq.gz" label="Single-end reads" />
0
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156 <repeat name="mp_repeat" title="Mate-pair library" help="The mate-pair libraries are used only for scaffolding and do not contribute towards the consensus sequence (mp)">
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157 <expand macro="reads_conditional" />
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158 </repeat>
5
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159 <param name="long_seqs" argument="long" type="data" multiple="true" optional="true" format="fasta,fastq,fastq.gz" label="Long sequences" help="Long sequence libraries are used only for rescaffolding and do not contribute towards the consensus sequence" />
2
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160 <param argument="k" type="integer" value="41" label="K-mer length (in bp)" help="The length of a k-mer (when -K is not set) or the span of a k-mer pair (when K is set)" />
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161 <param argument="K" type="integer" value="" optional="true" label="The length (in bp) of a single k-mer in a k-mer pair" help="Optional" />
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162 <param argument="q" type="integer" value="3" max="40" optional="true" label="Minimum base quality when trimming" help="Trim bases from the ends of reads whose quality is less than this value" />
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163 <param argument="Q" type="integer" value="0" max="40" optional="true" label="Minimum base quality" help="Mask all bases of reads whose quality is less than this value as 'N'" />
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164 <param argument="e" type="integer" value="" min="0" optional="true" label="Minimum erosion k-mer coverage" help="Erode bases at the ends of blunt contigs with coverage less than this value. Defaults to round(sqrt(median))" />
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165 <param argument="E" type="integer" value="" min="0" optional="true" label="Minimum erosion k-mer coverage per strand" help="Erode bases at the ends of blunt contigs with coverage less than this value on either strand. Defaults to 1 if sqrt(median) &gt; 2 else 0" />
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166 <param argument="t" type="integer" value="" optional="true" label="Maximum length of blunt contigs to trim" help="Defaults to the value of k" />
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167 <param argument="c" type="float" value="" optional="true" label="Minimum mean k-mer coverage of a unitig" help="Defaults to sqrt(median)" />
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168 <param argument="b" type="integer" value="" optional="true" label="Maximum length of a bubble (in bp)" help="abyss-pe has two bubble popping stages. The default limits are 3*k bp for ABYSS and 10000 bp for PopBubbles" />
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169 <param argument="SS" type="boolean" label="Assemble in strand-specific mode" help="Requires that all libraries are strand-specific RNA-Seq libraries. Assumes that the first read in a read pair is reveresed with respect to the transcripts sequenced" />
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170 <param argument="m" type="integer" value="50" min="0" optional="true" label="Minimum overlap of two unitigs (in bp)" />
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171 <param argument="p" type="float" value="0.9" optional="true" label="Minimum sequence identity of a bubble" />
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172 <param argument="a" type="integer" value="2" min="0" optional="true" label="Maximum number of branches of a bubble" />
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173 <param argument="l" type="integer" value="" min="1" optional="true" label="Minimum alignment length of a read (in bp)" help="Defaults to the value of k" />
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174 <param argument="s" type="integer" value="200" min="0" optional="true" label="Minimum unitig length required for building contigs (in bp)" help="The seed length should be at least twice the value of k. If more sequence is assembled than the expected genome size, try increasing this value" />
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175 <param argument="n" type="integer" value="10" min="0" optional="true" label="Minimum number of pairs required for building contigs" />
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176 <param argument="d" type="integer" value="6" min="0" optional="true" label="Allowable error of a distance estimate (in bp)" />
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177 <param argument="S" type="integer" value="" min="0" optional="true" label="Minimum contig length required for building scaffolds (in bp)" help="Defaults to the value of s" />
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178 <param argument="N" type="integer" value="" min="0" optional="true" label="Minimum number of pairs required for building scaffolds" help="Defaults to the value of n" />
0
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179 </inputs>
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180
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181 <outputs>
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182 <data name="unitigs" format="fasta" label="${tool.name} on ${on_string}: unitigs" from_work_dir="abyss-unitigs.fa" />
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183 <data name="contigs_outfile" format="fasta" label="${tool.name} on ${on_string}: contigs" from_work_dir="abyss-contigs.fa">
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184 <filter>lib_repeat</filter>
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185 </data>
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186 <data name="scaffolds" format="fasta" label="${tool.name} on ${on_string}: scaffolds" from_work_dir="abyss-scaffolds.fa">
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187 <filter>lib_repeat or mp_repeat</filter>
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188 </data>
1
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189 <data name="long_scaffolds" format="fasta" label="${tool.name} on ${on_string}: scaffolds" from_work_dir="abyss-long-scaffs.fa">
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190 <filter>long_seqs</filter>
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191 </data>
0
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192 <data name="bubbles" format="fasta" label="${tool.name} on ${on_string}: bubbles" from_work_dir="abyss-bubbles.fa" />
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193 <data name="indels" format="fasta" label="${tool.name} on ${on_string}: indels" from_work_dir="abyss-indel.fa" />
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194 <data name="coverage_histogram_outfile" format="tabular" label="${tool.name} on ${on_string}: coverage histogram" from_work_dir="coverage.hist" />
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195 <data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats" from_work_dir="abyss-stats.tab" />
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196 </outputs>
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197
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198 <tests>
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199 <test>
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200 <repeat name="lib_repeat">
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201 <conditional name="reads">
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202 <param name="reads_selector" value="paired" />
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203 <param name="reads1" ftype="fastqsanger" value="assembly_sample-R1.fastq.gz" />
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204 <param name="reads2" ftype="fastqsanger" value="assembly_sample-R2.fastq.gz" />
0
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205 </conditional>
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206 </repeat>
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207 <param name="k" value="50" />
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208 <output name="unitigs" file="abyss-unitigs1.fa" />
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209 <output name="contigs_outfile" file="abyss-contigs1.fa" />
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210 <output name="scaffolds" file="abyss-scaffolds1.fa" />
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211 <output name="bubbles" file="empty_file.fasta" />
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212 <output name="indels" file="empty_file.fasta" />
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213 <output name="coverage_histogram_outfile" file="coverage1.hist" />
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214 <output name="stats" file="abyss-stats1.tab" />
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215 </test>
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216 <test>
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217 <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq.gz,assembly_sample-R2.fastq.gz" />
0
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218 <param name="k" value="50" />
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219 <output name="unitigs" file="abyss-unitigs2.fa" />
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220 <output name="bubbles" file="empty_file.fasta" />
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221 <output name="indels" file="empty_file.fasta" />
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222 <output name="coverage_histogram_outfile" file="coverage2.hist" />
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223 <output name="stats" file="abyss-stats2.tab" />
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224 </test>
1
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225 <test>
5
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226 <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq.gz,assembly_sample-R2.fastq.gz" />
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227 <param name="long_seqs" ftype="fastqsanger" value="assembly_sample-R2.fastq.gz" />
1
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228 <param name="k" value="50" />
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229 <output name="unitigs" file="abyss-unitigs3.fa" />
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230 <output name="long_scaffolds" file="abyss-long-scaffolds3.fa" />
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231 <output name="bubbles" file="empty_file.fasta" />
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232 <output name="indels" file="empty_file.fasta" />
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233 <output name="coverage_histogram_outfile" file="coverage3.hist" />
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234 <output name="stats" file="abyss-stats3.tab" />
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235 </test>
0
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236 </tests>
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237 <help>
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238 **What it does**
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239
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240 `ABySS`_ is a de novo sequence assembler intended for short paired-end reads and large genomes.
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241
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242 **Input**
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243
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244 Input files should be FASTA or FASTQ files.
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245
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246 For paired reads, a pair of reads must be named with the suffixes /1 and /2 to identify the first and second read, or the reads may be named identically. The paired reads may be in separate files or interleaved in a single file.
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247
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248 At least a paired-end library or a single-end library must be provided.
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249
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250 Contigs are generated only if at least a paired-end library is provided. Scaffolds are generated only if at least a paired-end library or a mate-pair library is provided.
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251
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252 **Description**
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253
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254 This tool performs the complete ABySS pipeline using abyss-pe, described in https://github.com/bcgsc/abyss/blob/master/doc/flowchart.pdf .
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255
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256 **License and citation**
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257
1
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258 This Galaxy tool is Copyright © 2015-2016 `Earlham Institute`_ and is released under the `MIT license`_.
0
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259
1
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260 .. _Earlham Institute: http://www.earlham.ac.uk/
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261 .. _MIT license: https://opensource.org/licenses/MIT
0
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262
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263 You can use this tool only if you agree to the license terms of: `ABySS`_.
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264
3
f4fb67b97a63 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
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265 .. _ABySS: https://github.com/bcgsc/abyss
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f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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266 </help>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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267 <citations>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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268 <citation type="doi">10.1101/gr.089532.108</citation>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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269 </citations>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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270 </tool>