Mercurial > repos > nml > spades
annotate spades.xml @ 2:e37014a072e9 draft
planemo upload commit 733f396b6a4397c3b133bcb6fb3c10f5970db230-dirty
author | nml |
---|---|
date | Tue, 31 May 2016 15:43:30 -0400 |
parents | 80f079961dc9 |
children | 6dff6ed33cd7 |
rev | line source |
---|---|
2
e37014a072e9
planemo upload commit 733f396b6a4397c3b133bcb6fb3c10f5970db230-dirty
nml
parents:
1
diff
changeset
|
1 <tool id="spades" name="spades" version="1.3.1"> |
0
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
2 <description>SPAdes genome assembler for regular and single-cell projects</description> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
3 <requirements> |
2
e37014a072e9
planemo upload commit 733f396b6a4397c3b133bcb6fb3c10f5970db230-dirty
nml
parents:
1
diff
changeset
|
4 <requirement type="package" version="3.8.0">spades</requirement> |
0
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
5 </requirements> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
6 <command interpreter="perl">spades.pl |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
7 $out_contigs |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
8 $out_contig_stats |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
9 $out_scaffolds |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
10 $out_scaffold_stats |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
11 $out_log |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
12 |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
13 ## if the first library file is a paired-collection, use the key as the name |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
14 #if $libraries[0].files[0].file_type.type == "paired-collection": |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
15 $libraries[0].files[0].file_type.fastq_collection.name |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
16 #else: |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
17 NODE |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
18 #end if |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
19 ## A real command looks like: spades.py -k 21,33,55,77,99,127 --careful -1 Y.fastq.gz -2 X.fastq.gz -t 24 -o output |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
20 spades.py |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
21 ## Forces unzipped output, faster |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
22 --disable-gzip-output |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
23 $sc |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
24 $onlyassembler |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
25 $careful |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
26 -t \${GALAXY_SLOTS:-16} |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
27 -k "$kmers" |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
28 |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
29 #if $cov.state == "auto": |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
30 --cov-cutoff 'auto' |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
31 #elif $cov.state == "value": |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
32 --cov-cutoff '$cov.cutoff' |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
33 #end if |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
34 |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
35 $iontorrent |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
36 |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
37 ## Sequence files, libraries |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
38 #for $i, $library in enumerate( $libraries ) |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
39 #set num=$i+1 |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
40 #if str( $library.lib_type ) == "paired_end": |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
41 #set prefix = 'pe' |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
42 #elif str( $library.lib_type ) == "mate_paired": |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
43 #set prefix = 'mp' |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
44 #elif str( $library.lib_type ) == "nxmate_paired": |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
45 #set prefix = 'nxmate' |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
46 #else: |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
47 #set prefix = 'hqmp' |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
48 #end if |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
49 --$prefix$num-$library.orientation |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
50 #for $file in $library.files |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
51 #if $file.file_type.type == "separate" |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
52 --$prefix$num-1 fastq:$file.file_type.fwd_reads |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
53 --$prefix$num-2 fastq:$file.file_type.rev_reads |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
54 #elif $file.file_type.type == "interleaved" |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
55 --$prefix$num-12 fastq:$file.file_type.interleaved_reads |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
56 #elif $file.file_type.type == "unpaired" |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
57 --$prefix$num-s fastq:$file.file_type.unpaired_reads |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
58 #elif $file.file_type.type == "paired-collection" |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
59 --$prefix$num-1 fastq:$file.file_type.fastq_collection.forward |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
60 --$prefix$num-2 fastq:$file.file_type.fastq_collection.reverse |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
61 #end if |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
62 #end for |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
63 #end for |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
64 ## PacBio reads |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
65 #for $i, $pacbiolib in enumerate( $pacbio ) |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
66 --pacbio fastq:$pacbiolib.pacbio_reads |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
67 #end for |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
68 ## Nanopore |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
69 #for $i, $nanoporelib in enumerate( $nanopore ) |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
70 --nanopore fastq:$nanoporelib.nanopore_reads |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
71 #end for |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
72 ## Sanger |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
73 #for $i, $sangerlib in enumerate( $sanger ) |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
74 --sanger $sangerlib.file_type.type:$sangerlib.file_type.sanger_reads |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
75 #end for |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
76 ## Contigs |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
77 #for $i, $trustedcontigs in enumerate( $trustedcontigs ) |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
78 --trusted-contigs $trustedcontigs.file_type.type:$trustedcontigs.file_type.trusted_contigs |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
79 #end for |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
80 #for $i, $untrustedcontigs in enumerate( $untrustedcontigs ) |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
81 --untrusted-contigs $untrustedcontigs.file_type.type:$untrustedcontigs.file_type.untrusted_contigs |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
82 #end for |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
83 </command> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
84 <inputs> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
85 <param name="sc" type="boolean" truevalue="--sc" falsevalue="" label="Single-cell?" help="This option is required for MDA (single-cell) data."> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
86 <option value="false">No</option> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
87 <option value="true">Yes</option> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
88 </param> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
89 <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
90 <param name="careful" type="boolean" truevalue="--careful" falsevalue="" checked="True" label="Careful correction?" help="Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector – a post processing tool, which uses BWA tool (comes with SPAdes)." /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
91 <param name="kmers" type="text" label="K-mers to use, separated by commas" value="21,33,55" help="Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55." > |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
92 |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
93 </param> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
94 <conditional name="cov"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
95 <param name="state" type="select" label="Coverage Cutoff"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
96 <option value="off">Off</option> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
97 <option value="value">User Specific</option> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
98 <option value="auto">Auto</option> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
99 </param> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
100 <when value="off"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
101 </when> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
102 <when value="value"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
103 <param name="cutoff" type="float" label="Coverage cutoff value" value="" help="coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
104 </when> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
105 <when value="auto"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
106 </when> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
107 </conditional> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
108 |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
109 |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
110 |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
111 <param name="iontorrent" type="boolean" truevalue="--iontorrent" falsevalue="" checked="False" label="Libraries are IonTorrent reads?" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
112 <!-- Reads --> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
113 <repeat name="libraries" title="Libraries" min="1" help="It is not possible to specify only mate-pair libraries. Scaffolds are not produced if neither a paired-end nor a mate-pair library is provided."> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
114 <param name="lib_type" type="select" label="Library type"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
115 <option value="paired_end">Paired-end / Single reads</option> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
116 <option value="mate_paired">Mate pairs</option> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
117 <option value="high_mate_paired">High Quality Mate pairs</option> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
118 <option value="nxmate_paired">Lucigen NxMate pairs</option> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
119 </param> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
120 <param name="orientation" type="select" label="Orientation"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
121 <option value="fr" selected="true">-> <- (fr)</option> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
122 <option value="rf"><- -> (rf)</option> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
123 <option value="ff">-> -> (ff)</option> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
124 </param> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
125 <repeat name="files" title="Files" min="1"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
126 <conditional name="file_type"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
127 <param name="type" type="select" label="Select file format"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
128 <option value="separate">Separate input files</option> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
129 <option value="interleaved">Interleaved files</option> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
130 <option value="unpaired">Unpaired/Single reads</option> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
131 <option value="paired-collection">Paired List Collection</option> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
132 </param> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
133 <when value="separate"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
134 <param name="fwd_reads" type="data" format="fastq" label="Forward reads" help="FASTQ format" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
135 <param name="rev_reads" type="data" format="fastq" label="Reverse reads" help="FASTQ format" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
136 </when> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
137 <when value="interleaved"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
138 <param name="interleaved_reads" type="data" format="fastq" label="Interleaved paired reads" help="FASTQ format" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
139 </when> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
140 <when value="unpaired"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
141 <param name="unpaired_reads" type="data" format="fastq" label="Unpaired reads" help="FASTQ format" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
142 </when> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
143 <when value="paired-collection"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
144 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastq" collection_type="paired" help="FASTQ format" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
145 </when> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
146 </conditional> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
147 </repeat> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
148 </repeat> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
149 <!-- PacBio --> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
150 <repeat name="pacbio" title="PacBio CLR reads"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
151 <param name="pacbio_reads" type="data" format="fastq" label="PacBio CLR reads." help="FASTQ format. For PacBio pre-corrected or CCS reads, use single reads above." /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
152 </repeat> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
153 <!-- Nanopore --> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
154 <repeat name="nanopore" title="Nanopore reads"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
155 <param name="nanopore_reads" type="data" format="fastq" label="Nanopore reads." help="FASTQ format. For Nanopore, use single reads above." /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
156 </repeat> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
157 <!-- Sanger --> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
158 <repeat name="sanger" title="Sanger reads"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
159 <conditional name="file_type"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
160 <param name="type" type="select" label="Select file format" help="No read correction is done on Sanger reads, no need to provide quality information."> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
161 <option value="fasta">fasta</option> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
162 <option value="fastq">fastq</option> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
163 </param> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
164 <when value="fasta"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
165 <param name="sanger_reads" type="data" format="fasta" label="Sanger reads" help="FASTA format" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
166 </when> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
167 <when value="fastq"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
168 <param name="sanger_reads" type="data" format="fastq" label="Sanger reads" help="FASTQ format" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
169 </when> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
170 </conditional> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
171 </repeat> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
172 <!-- Contigs --> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
173 <repeat name="trustedcontigs" title="Trusted contigs" help="Reliable contigs of the same genome, which are likely to have no misassemblies and small rate of other errors (e.g. mismatches and indels). This option is not intended for contigs of the related species."> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
174 <conditional name="file_type"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
175 <param name="type" type="select" label="Select file format"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
176 <option value="fasta">fasta</option> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
177 <option value="fastq">fastq</option> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
178 </param> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
179 <when value="fasta"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
180 <param name="trusted_contigs" type="data" format="fasta" label="Trusted contigs" help="FASTA format" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
181 </when> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
182 <when value="fastq"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
183 <param name="trusted_contigs" type="data" format="fastq" label="Trusted contigs" help="FASTQ format" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
184 </when> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
185 </conditional> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
186 </repeat> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
187 <repeat name="untrustedcontigs" title="Untrusted contigs" help="Contigs of the same genome, quality of which is average or unknown. Contigs of poor quality can be used but may introduce errors in the assembly. This option is also not intended for contigs of the related species."> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
188 <conditional name="file_type"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
189 <param name="type" type="select" label="Select file format"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
190 <option value="fasta">fasta</option> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
191 <option value="fastq">fastq</option> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
192 </param> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
193 <when value="fasta"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
194 <param name="untrusted_contigs" type="data" format="fasta" label="Untrusted contigs" help="FASTA format" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
195 </when> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
196 <when value="fastq"> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
197 <param name="untrusted_contigs" type="data" format="fastq" label="Untrusted contigs" help="FASTQ format" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
198 </when> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
199 </conditional> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
200 </repeat> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
201 </inputs> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
202 <outputs> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
203 <data name="out_contigs" format="fasta" label="SPAdes contigs (fasta)" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
204 <data name="out_contig_stats" format="tabular" label="SPAdes contig stats" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
205 <data name="out_scaffolds" format="fasta" label="SPAdes scaffolds (fasta)" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
206 <data name="out_scaffold_stats" format="tabular" label="SPAdes scaffold stats" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
207 <data name="out_log" format="txt" label="SPAdes log" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
208 </outputs> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
209 <tests> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
210 <test> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
211 <param name="sc" value="false" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
212 <param name="careful" value="false" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
213 <param name="kmers" value="33,55" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
214 <param name="lib_type" value="paired_end" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
215 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
216 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
217 <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" /> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
218 </test> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
219 </tests> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
220 <help> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
221 **What it does** |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
222 |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
223 SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. See http://bioinf.spbau.ru/en/spades for more details on SPAdes. |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
224 |
2
e37014a072e9
planemo upload commit 733f396b6a4397c3b133bcb6fb3c10f5970db230-dirty
nml
parents:
1
diff
changeset
|
225 This wrapper runs SPAdes 3.8, collects the output, and throws away all the temporary files. It also produces a tab file with contig names, length and coverage. |
0
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
226 |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
227 **License** |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
228 |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
229 SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2. |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
230 |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
231 This wrapper is copyrighted by Philip Mabon and is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
232 |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
233 This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
234 |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
235 You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/. |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
236 |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
237 ** Acknowledgments ** |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
238 |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
239 Original wrapper developed by Lionel Guy. |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
240 |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
241 Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes. |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
242 |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
243 Nicola Soranzo fixed various bugs. |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
244 </help> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
245 <citations> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
246 <citation type="doi">10.1089/cmb.2012.0021</citation> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
247 </citations> |
009c00203195
planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff
changeset
|
248 </tool> |