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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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">-> &lt;- (fr)</option>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty
nml
parents:
diff changeset
122 <option value="rf">&lt;- -> (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>