Mercurial > repos > iuc > abyss

annotate abyss-pe.xml @ 5:fa5259cc561b 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 52c73f875aef9c4692b886e1a50d8124875e7dcb"
author iuc
date Fri, 19 Mar 2021 21:37:30 +0000
parents 3ce74eab308b
children 0e93176640ac
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
fa5259cc561b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 4
diff changeset
1 <tool id="abyss-pe" name="ABySS" version="@TOOL_VERSION@+galaxy1">
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>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
3 <macros>
4
3ce74eab308b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 5ecb0de2196e69548d74a88a4e3c1095ca9bfd16"
iuc
parents: 3
diff changeset
4 <token name="@TOOL_VERSION@">2.2.3</token>
0
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
5 <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
6 <conditional name="reads">
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
7 <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
8 <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
9 <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
10 <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
11 </param>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
12 <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
13 <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
14 <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
15 </when>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
16 <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
17 <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
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_il">
5
fa5259cc561b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 4
diff changeset
20 <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
21 </when>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
22 </conditional>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
23 </xml>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
24 </macros>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
25 <requirements>
2
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
26 <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
27 <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
28 </requirements>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
29 <stdio>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
30 <!-- 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
31 <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
32 <!-- 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
33 <regex match="Error:" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
34 <regex match="Exception:" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
35 </stdio>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
36 <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
37 <command>
2
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
38 abyss-pe
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
39 name=abyss
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
40 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
41 k=$k
1
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
parents: 0
diff changeset
42
2
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
43 #if str($K)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
44 K=$K
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
45 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
46 #if str($q)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
47 q=$q
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
48 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
49 #if str($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=$Q
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
51 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
52 #if str($e)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
53 e=$e
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
54 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
55 #if str($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=$E
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
57 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
58 #if str($t)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
59 t=$t
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
60 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
61 #if str($c)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
62 c=$c
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
63 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
64 #if str($b)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
65 b=$b
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 $SS
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
68 SS=--SS
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
69 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
70 #if str($m)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
71 m=$m
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
72 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
73 #if str($p)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
74 p=$p
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
75 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
76 #if str($a)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
77 a=$a
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
78 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
79 #if str($l)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
80 l=$l
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
81 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
82 #if str($s)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
83 s=$s
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
84 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
85 #if str($n)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
86 n=$n
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
87 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
88 #if str($d)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
89 d=$d
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
90 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
91 #if str($S)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
92 S=$S
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
93 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
94 #if str($N)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
95 N=$N
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
96 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
97 #if $lib_repeat
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
98 lib='
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
99 #for $i in range(len($lib_repeat))
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
100 lib$i
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
101 #end for
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
102 '
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
103 #for $i, $v in enumerate($lib_repeat)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
104 #if $v.reads.reads_selector == 'paired'
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
105 lib${i}='${v.reads.reads1} ${v.reads.reads2}'
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
106 #elif $v.reads.reads_selector == 'paired_collection'
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
107 lib${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}'
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
108 #else
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
109 lib${i}='${v.reads.reads_il}'
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
110 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
111 #end for
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
112 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
113 #if str($se_reads) != 'None'
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
114 se='
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
115 #for $v in $se_reads
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
116 $v
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
117 #end for
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
118 '
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
119 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
120 #if $mp_repeat
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
121 mp='
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
122 #for $i in range(len($mp_repeat))
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
123 mp$i
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
124 #end for
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
125 '
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
126 #for $i, $v in enumerate($mp_repeat)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
127 #if $v.reads.reads_selector == 'paired'
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
128 mp${i}='${v.reads.reads1} ${v.reads.reads2}'
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
129 #elif $v.reads.reads_selector == 'paired_collection'
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
130 mp${i}='${v.reads.reads_coll.forward} ${v.reads.reads_coll.reverse}'
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
131 #else
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
132 mp${i}='${v.reads.reads_il}'
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
133 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
134 #end for
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
135 #end if
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
136 #if str($long_seqs) != 'None'
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
137 long='
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
138 #for $i in range(len($long_seqs))
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
139 long$i
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
140 #end for
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
141 '
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
142 #for $i, $v in enumerate($long_seqs)
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
143 long${i}='$v'
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
144 #end for
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
145 #end if
0
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
146 </command>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
147
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
148 <inputs>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
149 <repeat name="lib_repeat" title="Paired-end library" help="(lib)">
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
150 <expand macro="reads_conditional" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
151 </repeat>
5
fa5259cc561b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 4
diff changeset
152 <param name="se_reads" argument="se" type="data" multiple="true" optional="true" format="fasta,fastq,fastq.gz" label="Single-end reads" />
0
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
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)">
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
154 <expand macro="reads_conditional" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
155 </repeat>
5
fa5259cc561b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 4
diff changeset
156 <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
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
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)" />
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
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" />
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
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" />
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
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'" />
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
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))" />
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
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" />
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
163 <param argument="t" type="integer" value="" optional="true" label="Maximum length of blunt contigs to trim" help="Defaults to the value of k" />
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
164 <param argument="c" type="float" value="" optional="true" label="Minimum mean k-mer coverage of a unitig" help="Defaults to sqrt(median)" />
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
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" />
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
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" />
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
167 <param argument="m" type="integer" value="50" min="0" optional="true" label="Minimum overlap of two unitigs (in bp)" />
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
168 <param argument="p" type="float" value="0.9" optional="true" label="Minimum sequence identity of a bubble" />
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
169 <param argument="a" type="integer" value="2" min="0" optional="true" label="Maximum number of branches of a bubble" />
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
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" />
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
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" />
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
172 <param argument="n" type="integer" value="10" min="0" optional="true" label="Minimum number of pairs required for building contigs" />
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
173 <param argument="d" type="integer" value="6" min="0" optional="true" label="Allowable error of a distance estimate (in bp)" />
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
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" />
2b89471cca20 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0356fbc3ad22b122375a98ff07ed6eff51141852"
iuc
parents: 1
diff changeset
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" />
0
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
176 </inputs>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
177
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
178 <outputs>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
179 <data name="unitigs" format="fasta" label="${tool.name} on ${on_string}: unitigs" from_work_dir="abyss-unitigs.fa" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
180 <data name="contigs_outfile" format="fasta" label="${tool.name} on ${on_string}: contigs" from_work_dir="abyss-contigs.fa">
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
181 <filter>lib_repeat</filter>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
182 </data>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
183 <data name="scaffolds" format="fasta" label="${tool.name} on ${on_string}: scaffolds" from_work_dir="abyss-scaffolds.fa">
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
184 <filter>lib_repeat or mp_repeat</filter>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
185 </data>
1
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
parents: 0
diff changeset
186 <data name="long_scaffolds" format="fasta" label="${tool.name} on ${on_string}: scaffolds" from_work_dir="abyss-long-scaffs.fa">
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
parents: 0
diff changeset
187 <filter>long_seqs</filter>
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
parents: 0
diff changeset
188 </data>
0
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
189 <data name="bubbles" format="fasta" label="${tool.name} on ${on_string}: bubbles" from_work_dir="abyss-bubbles.fa" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
190 <data name="indels" format="fasta" label="${tool.name} on ${on_string}: indels" from_work_dir="abyss-indel.fa" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
191 <data name="coverage_histogram_outfile" format="tabular" label="${tool.name} on ${on_string}: coverage histogram" from_work_dir="coverage.hist" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
192 <data name="stats" format="tabular" label="${tool.name} on ${on_string}: stats" from_work_dir="abyss-stats.tab" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
193 </outputs>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
194
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
195 <tests>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
196 <test>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
197 <repeat name="lib_repeat">
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
198 <conditional name="reads">
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
199 <param name="reads_selector" 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
200 <param name="reads1" ftype="fastqsanger" value="assembly_sample-R1.fastq.gz" />
fa5259cc561b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 4
diff changeset
201 <param name="reads2" ftype="fastqsanger" value="assembly_sample-R2.fastq.gz" />
0
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
202 </conditional>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
203 </repeat>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
204 <param name="k" value="50" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
205 <output name="unitigs" file="abyss-unitigs1.fa" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
206 <output name="contigs_outfile" file="abyss-contigs1.fa" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
207 <output name="scaffolds" file="abyss-scaffolds1.fa" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
208 <output name="bubbles" file="empty_file.fasta" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
209 <output name="indels" file="empty_file.fasta" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
210 <output name="coverage_histogram_outfile" file="coverage1.hist" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
211 <output name="stats" file="abyss-stats1.tab" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
212 </test>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
213 <test>
5
fa5259cc561b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 4
diff changeset
214 <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq.gz,assembly_sample-R2.fastq.gz" />
0
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
215 <param name="k" value="50" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
216 <output name="unitigs" file="abyss-unitigs2.fa" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
217 <output name="bubbles" file="empty_file.fasta" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
218 <output name="indels" file="empty_file.fasta" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
219 <output name="coverage_histogram_outfile" file="coverage2.hist" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
220 <output name="stats" file="abyss-stats2.tab" />
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
221 </test>
1
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
parents: 0
diff changeset
222 <test>
5
fa5259cc561b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 4
diff changeset
223 <param name="se_reads" ftype="fastqsanger" value="assembly_sample-R1.fastq.gz,assembly_sample-R2.fastq.gz" />
fa5259cc561b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 52c73f875aef9c4692b886e1a50d8124875e7dcb"
iuc
parents: 4
diff changeset
224 <param name="long_seqs" ftype="fastqsanger" value="assembly_sample-R2.fastq.gz" />
1
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
parents: 0
diff changeset
225 <param name="k" value="50" />
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
parents: 0
diff changeset
226 <output name="unitigs" file="abyss-unitigs3.fa" />
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
parents: 0
diff changeset
227 <output name="long_scaffolds" file="abyss-long-scaffolds3.fa" />
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
parents: 0
diff changeset
228 <output name="bubbles" file="empty_file.fasta" />
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
parents: 0
diff changeset
229 <output name="indels" file="empty_file.fasta" />
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
parents: 0
diff changeset
230 <output name="coverage_histogram_outfile" file="coverage3.hist" />
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
parents: 0
diff changeset
231 <output name="stats" file="abyss-stats3.tab" />
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
parents: 0
diff changeset
232 </test>
0
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
233 </tests>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
234 <help>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
235 **What it does**
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
236
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
237 `ABySS`_ is a de novo sequence assembler intended for short paired-end reads and large genomes.
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
238
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
239 **Input**
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
240
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
241 Input files should be FASTA or FASTQ files.
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
242
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
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.
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
244
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
245 At least a paired-end library or a single-end library must be provided.
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
246
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
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.
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
248
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
249 **Description**
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
250
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
251 This tool performs the complete ABySS pipeline using abyss-pe, described in https://github.com/bcgsc/abyss/blob/master/doc/flowchart.pdf .
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
252
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
253 **License and citation**
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
254
1
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
parents: 0
diff changeset
255 This Galaxy tool is Copyright © 2015-2016 `Earlham Institute`_ and is released under the `MIT license`_.
0
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
256
1
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
parents: 0
diff changeset
257 .. _Earlham Institute: http://www.earlham.ac.uk/
0a5c7992b1ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
iuc
parents: 0
diff changeset
258 .. _MIT license: https://opensource.org/licenses/MIT
0
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
259
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
260 You can use this tool only if you agree to the license terms of: `ABySS`_.
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
261
3
f4fb67b97a63 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
iuc
parents: 2
diff changeset
262 .. _ABySS: https://github.com/bcgsc/abyss
0
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
263 </help>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
264 <citations>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
265 <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
iuc
parents:
diff changeset
266 </citations>
f048033da666 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
diff changeset
267 </tool>