Mercurial > repos > iuc > abyss

annotate abyss-pe.xml @ 8:e05fde246daf 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 0356fbc3ad22b122375a98ff07ed6eff51141852"
author iuc
date Sun, 01 Sep 2019 11:57:10 -0400
parents 51ca82f3ffaf
children a63fabfcaf9a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
1 <tool id="abyss-pe" name="ABySS" version="@TOOL_VERSION@">
6
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
2 <description>de novo sequence assembler</description>
0
1d0f1274d999 Uploaded
iuc
parents:
diff changeset
3 <macros>
8
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
4 <token name="@TOOL_VERSION@">2.2.1</token>
6
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
5 <xml name="reads_conditional">
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
6 <conditional name="reads">
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
7 <param name="reads_selector" type="select" label="Type of paired-end datasets">
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
8 <option value="paired">2 separate datasets</option>
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
9 <option value="paired_collection">1 paired dataset collection</option>
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
10 <option value="paired_il">1 dataset of interleaved reads</option>
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
11 </param>
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
12 <when value="paired">
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
13 <param name="reads1" type="data" format="fasta,fastq,fastqsanger,fastqillumina" label="Paired-end reads 1" />
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
14 <param name="reads2" type="data" format="fasta,fastq,fastqsanger,fastqillumina" label="Paired-end reads 2" />
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
15 </when>
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
16 <when value="paired_collection">
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
17 <param name="reads_coll" type="data_collection" collection_type="paired" format="fasta,fastq,fastqsanger,fastqillumina" label="Paired-end reads collection" />
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
18 </when>
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
19 <when value="paired_il">
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
20 <param name="reads_il" type="data" format="fasta,fastq,fastqsanger,fastqillumina" label="Interleaved paired-end reads" />
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
21 </when>
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
22 </conditional>
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
23 </xml>
0
1d0f1274d999 Uploaded
iuc
parents:
diff changeset
24 </macros>
6
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
25 <requirements>
8
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
26 <requirement type="package" version="@TOOL_VERSION@">abyss</requirement>
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
27 <requirement type="package" version="0.7.17">bwa</requirement>
6
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
28 </requirements>
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
29 <stdio>
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
30 <!-- Anything other than zero is an error -->
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
31 <exit_code range="1:" />
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
32 <!-- In case the return code has not been set propery check stderr too -->
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
33 <regex match="Error:" />
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
34 <regex match="Exception:" />
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
35 </stdio>
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
36 <version_command>ABYSS --version | head -n 1</version_command>
1e19058d6c0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 5
diff changeset
37 <command>
8
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
38 abyss-pe
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
39 name=abyss
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
40 j=\${GALAXY_SLOTS:-1}
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
41 k=$k
7
51ca82f3ffaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
parents: 6
diff changeset
42
8
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
43 #if str($K)
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
44 K=$K
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
45 #end if
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
46 #if str($q)
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
47 q=$q
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
48 #end if
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
49 #if str($Q)
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
50 Q=$Q
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
51 #end if
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
52 #if str($e)
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
53 e=$e
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
54 #end if
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
55 #if str($E)
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
56 E=$E
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
57 #end if
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
58 #if str($t)
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
59 t=$t
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
60 #end if
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
61 #if str($c)
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
62 c=$c
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
63 #end if
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
64 #if str($b)
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
65 b=$b
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
66 #end if
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
67 #if $SS
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
68 SS=--SS
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
69 #end if
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
70 #if str($m)
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
71 m=$m
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
72 #end if
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
73 #if str($p)
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
74 p=$p
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
75 #end if
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
76 #if str($a)
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
77 a=$a
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
78 #end if
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
79 #if str($l)
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
80 l=$l
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
81 #end if
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
82 #if str($s)
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
83 s=$s
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
84 #end if
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
85 #if str($n)
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
86 n=$n
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
87 #end if
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
88 #if str($d)
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
89 d=$d
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
90 #end if
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
91 #if str($S)
e05fde246daf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 7
diff changeset
92 S=$S
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93 #end if
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94 #if str($N)
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95 N=$N
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96 #end if
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97 #if $lib_repeat
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98 lib='
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99 #for $i in range(len($lib_repeat))
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100 lib$i
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101 #end for
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102 '
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103 #for $i, $v in enumerate($lib_repeat)
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104 #if $v.reads.reads_selector == 'paired'
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105 lib${i}='${v.reads.reads1} ${v.reads.reads2}'
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106 #elif $v.reads.reads_selector == 'paired_collection'
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107 lib${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}'
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108 #else
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109 lib${i}='${v.reads.reads_il}'
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110 #end if
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111 #end for
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112 #end if
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113 #if str($se_reads) != 'None'
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114 se='
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115 #for $v in $se_reads
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116 $v
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117 #end for
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118 '
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119 #end if
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120 #if $mp_repeat
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121 mp='
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122 #for $i in range(len($mp_repeat))
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123 mp$i
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124 #end for
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125 '
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126 #for $i, $v in enumerate($mp_repeat)
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127 #if $v.reads.reads_selector == 'paired'
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128 mp${i}='${v.reads.reads1} ${v.reads.reads2}'
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129 #elif $v.reads.reads_selector == 'paired_collection'
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130 mp${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}'
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131 #else
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132 mp${i}='${v.reads.reads_il}'
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133 #end if
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134 #end for
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135 #end if
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136 #if str($long_seqs) != 'None'
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137 long='
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138 #for $i in range(len($long_seqs))
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139 long$i
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140 #end for
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141 '
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142 #for $i, $v in enumerate($long_seqs)
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143 long${i}='$v'
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144 #end for
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145 #end if
0
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146 </command>
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147
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148 <inputs>
6
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149 <repeat name="lib_repeat" title="Paired-end library" help="(lib)">
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150 <expand macro="reads_conditional" />
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151 </repeat>
8
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152 <param name="se_reads" argument="se" type="data" multiple="true" optional="true" format="fasta,fastq,fastqsanger,fastqillumina" label="Single-end reads" />
6
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153 <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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154 <expand macro="reads_conditional" />
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155 </repeat>
8
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156 <param name="long_seqs" argument="long" type="data" multiple="true" optional="true" format="fasta,fastq,fastqsanger,fastqillumina" label="Long sequences" help="Long sequence libraries are used only for rescaffolding and do not contribute towards the consensus sequence" />
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157 <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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158 <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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159 <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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160 <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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161 <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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162 <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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163 <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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164 <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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165 <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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166 <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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167 <param argument="m" type="integer" value="50" min="0" optional="true" label="Minimum overlap of two unitigs (in bp)" />
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168 <param argument="p" type="float" value="0.9" optional="true" label="Minimum sequence identity of a bubble" />
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169 <param argument="a" type="integer" value="2" min="0" optional="true" label="Maximum number of branches of a bubble" />
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170 <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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171 <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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172 <param argument="n" type="integer" value="10" min="0" optional="true" label="Minimum number of pairs required for building contigs" />
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173 <param argument="d" type="integer" value="6" min="0" optional="true" label="Allowable error of a distance estimate (in bp)" />
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174 <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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175 <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" />
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176 </inputs>
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177
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178 <outputs>
6
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179 <data name="unitigs" format="fasta" label="${tool.name} on ${on_string}: unitigs" from_work_dir="abyss-unitigs.fa" />
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180 <data name="contigs_outfile" format="fasta" label="${tool.name} on ${on_string}: contigs" from_work_dir="abyss-contigs.fa">
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181 <filter>lib_repeat</filter>
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182 </data>
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183 <data name="scaffolds" format="fasta" label="${tool.name} on ${on_string}: scaffolds" from_work_dir="abyss-scaffolds.fa">
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184 <filter>lib_repeat or mp_repeat</filter>
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185 </data>
7
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186 <data name="long_scaffolds" format="fasta" label="${tool.name} on ${on_string}: scaffolds" from_work_dir="abyss-long-scaffs.fa">
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187 <filter>long_seqs</filter>
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188 </data>
6
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189 <data name="bubbles" format="fasta" label="${tool.name} on ${on_string}: bubbles" from_work_dir="abyss-bubbles.fa" />
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190 <data name="indels" format="fasta" label="${tool.name} on ${on_string}: indels" from_work_dir="abyss-indel.fa" />
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191 <data name="coverage_histogram_outfile" format="tabular" label="${tool.name} on ${on_string}: coverage histogram" from_work_dir="coverage.hist" />
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192 <data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats" from_work_dir="abyss-stats.tab" />
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193 </outputs>
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194
6
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195 <tests>
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196 <test>
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197 <repeat name="lib_repeat">
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198 <conditional name="reads">
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199 <param name="reads_selector" value="paired" />
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200 <param name="reads1" ftype="fastqsanger" value="assembly_sample-R1.fastq" />
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201 <param name="reads2" ftype="fastqsanger" value="assembly_sample-R2.fastq" />
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202 </conditional>
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203 </repeat>
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204 <param name="k" value="50" />
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205 <output name="unitigs" file="abyss-unitigs1.fa" />
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206 <output name="contigs_outfile" file="abyss-contigs1.fa" />
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207 <output name="scaffolds" file="abyss-scaffolds1.fa" />
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208 <output name="bubbles" file="empty_file.fasta" />
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209 <output name="indels" file="empty_file.fasta" />
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210 <output name="coverage_histogram_outfile" file="coverage1.hist" />
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211 <output name="stats" file="abyss-stats1.tab" />
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212 </test>
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213 <test>
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214 <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq,assembly_sample-R2.fastq" />
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215 <param name="k" value="50" />
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216 <output name="unitigs" file="abyss-unitigs2.fa" />
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217 <output name="bubbles" file="empty_file.fasta" />
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218 <output name="indels" file="empty_file.fasta" />
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219 <output name="coverage_histogram_outfile" file="coverage2.hist" />
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220 <output name="stats" file="abyss-stats2.tab" />
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221 </test>
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222 <test>
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223 <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq,assembly_sample-R2.fastq" />
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224 <param name="long_seqs" ftype="fastqsanger" value="assembly_sample-R2.fastq" />
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225 <param name="k" value="50" />
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226 <output name="unitigs" file="abyss-unitigs3.fa" />
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227 <output name="long_scaffolds" file="abyss-long-scaffolds3.fa" />
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228 <output name="bubbles" file="empty_file.fasta" />
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229 <output name="indels" file="empty_file.fasta" />
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230 <output name="coverage_histogram_outfile" file="coverage3.hist" />
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231 <output name="stats" file="abyss-stats3.tab" />
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232 </test>
6
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233 </tests>
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234 <help>
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235 **What it does**
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236
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237 `ABySS`_ is a de novo sequence assembler intended for short paired-end reads and large genomes.
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238
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239 **Input**
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240
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241 Input files should be FASTA or FASTQ files.
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242
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243 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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244
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245 At least a paired-end library or a single-end library must be provided.
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246
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247 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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248
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249 **Description**
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250
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251 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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252
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253 **License and citation**
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254
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255 This Galaxy tool is Copyright © 2015-2016 `Earlham Institute`_ and is released under the `MIT license`_.
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256
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257 .. _Earlham Institute: http://www.earlham.ac.uk/
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258 .. _MIT license: https://opensource.org/licenses/MIT
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259
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260 You can use this tool only if you agree to the license terms of: `ABySS`_.
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261
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262 .. _ABySS: http://www.bcgsc.ca/platform/bioinfo/software/abyss
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263 </help>
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264 <citations>
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265 <citation type="doi">10.1101/gr.089532.108</citation>
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266 </citations>
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267 </tool>