annotate plasmidSPAdes.xml @ 0:27b90e43e2d8 draft

planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
author nml
date Mon, 06 Jun 2016 15:13:06 -0400
parents
children a415d510332b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
1 <tool id="plasmidspades" name="plasmidspades" version="1.0">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
2 <description>genome assembler for plasmids</description>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
3 <requirements>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
4 <requirement type="package" version="3.8.0">spades</requirement>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
5 </requirements>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
6 <command interpreter="perl">spades.pl
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
7 $out_contigs
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
8 $out_contig_stats
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
9 $out_scaffolds
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
10 $out_scaffold_stats
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
11 $out_log
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
12
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
13 ## if the first fileset is a paired-collection, use the key as the name
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
14 #if $files[0].file_type.type == "paired-collection":
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
15 $files[0].file_type.fastq_collection.name
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
16 #else:
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
17 NODE
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
18 #end if
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
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
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
20 spades.py
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
21 ## Forces unzipped output, faster
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
22 --disable-gzip-output
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
23 --plasmid
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
24 $onlyassembler
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
25 $careful
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
26 -t \${GALAXY_SLOTS:-16}
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
27 -k "$kmers"
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
28
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
29 #if $cov.state == "auto":
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
30 --cov-cutoff 'auto'
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
31 #elif $cov.state == "value":
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
32 --cov-cutoff '$cov.cutoff'
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
33 #end if
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
34
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
35 $iontorrent
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
36
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
37 ## Sequence files
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
38 #set num=1
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
39 #if str( $lib_type ) == "paired_end":
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
40 #set prefix = 'pe'
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
41 #elif str( $lib_type ) == "mate_paired":
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
42 #set prefix = 'mp'
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
43 #elif str( $lib_type ) == "nxmate_paired":
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
44 #set prefix = 'nxmate'
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
45 #else:
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
46 #set prefix = 'hqmp'
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
47 #end if
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
48 --$prefix$num-$orientation
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
49 #for $file in $files
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
50 #if $file.file_type.type == "separate"
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
51 --$prefix$num-1 fastq:$file.file_type.fwd_reads
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
52 --$prefix$num-2 fastq:$file.file_type.rev_reads
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
53 #elif $file.file_type.type == "interleaved"
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
54 --$prefix$num-12 fastq:$file.file_type.interleaved_reads
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
55 #elif $file.file_type.type == "unpaired"
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
56 --$prefix$num-s fastq:$file.file_type.unpaired_reads
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
57 #elif $file.file_type.type == "paired-collection"
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
58 --$prefix$num-1 fastq:$file.file_type.fastq_collection.forward
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
59 --$prefix$num-2 fastq:$file.file_type.fastq_collection.reverse
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
60 #end if
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
61 #end for
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
62
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
63 ## PacBio reads
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
64 #for $i, $pacbiolib in enumerate( $pacbio )
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
65 --pacbio fastq:$pacbiolib.pacbio_reads
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
66 #end for
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
67 ## Nanopore
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
68 #for $i, $nanoporelib in enumerate( $nanopore )
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
69 --nanopore fastq:$nanoporelib.nanopore_reads
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
70 #end for
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
71 ## Sanger
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
72 #for $i, $sangerlib in enumerate( $sanger )
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
73 --sanger $sangerlib.file_type.type:$sangerlib.file_type.sanger_reads
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
74 #end for
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
75 ## Contigs
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
76 #for $i, $trustedcontigs in enumerate( $trustedcontigs )
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
77 --trusted-contigs $trustedcontigs.file_type.type:$trustedcontigs.file_type.trusted_contigs
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
78 #end for
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
79 #for $i, $untrustedcontigs in enumerate( $untrustedcontigs )
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
80 --untrusted-contigs $untrustedcontigs.file_type.type:$untrustedcontigs.file_type.untrusted_contigs
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
81 #end for
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
82 </command>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
83 <inputs>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
84 <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
85 <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)." />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
86 <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." >
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
87
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
88 </param>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
89 <conditional name="cov">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
90 <param name="state" type="select" label="Coverage Cutoff">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
91 <option value="off">Off</option>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
92 <option value="value">User Specific</option>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
93 <option value="auto">Auto</option>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
94 </param>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
95 <when value="off">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
96 </when>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
97 <when value="value">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
98 <param name="cutoff" type="float" label="Coverage cutoff value" value="" help="coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
99 </when>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
100 <when value="auto">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
101 </when>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
102 </conditional>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
103
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
104
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
105
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
106 <param name="iontorrent" type="boolean" truevalue="--iontorrent" falsevalue="" checked="False" label="Libraries are IonTorrent reads?" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
107 <!-- Reads -->
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
108
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
109 <param name="lib_type" type="select" label="Library type">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
110 <option value="paired_end">Paired-end / Single reads</option>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
111 <option value="mate_paired">Mate pairs</option>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
112 <option value="high_mate_paired">High Quality Mate pairs</option>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
113 <option value="nxmate_paired">Lucigen NxMate pairs</option>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
114 </param>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
115 <param name="orientation" type="select" label="Orientation">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
116 <option value="fr" selected="true">-> &lt;- (fr)</option>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
117 <option value="rf">&lt;- -> (rf)</option>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
118 <option value="ff">-> -> (ff)</option>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
119 </param>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
120 <repeat name="files" title="Files" min="1">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
121 <conditional name="file_type">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
122 <param name="type" type="select" label="Select file format">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
123 <option value="separate">Separate input files</option>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
124 <option value="interleaved">Interleaved files</option>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
125 <option value="unpaired">Unpaired/Single reads</option>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
126 <option value="paired-collection">Paired List Collection</option>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
127 </param>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
128 <when value="separate">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
129 <param name="fwd_reads" type="data" format="fastq" label="Forward reads" help="FASTQ format" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
130 <param name="rev_reads" type="data" format="fastq" label="Reverse reads" help="FASTQ format" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
131 </when>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
132 <when value="interleaved">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
133 <param name="interleaved_reads" type="data" format="fastq" label="Interleaved paired reads" help="FASTQ format" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
134 </when>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
135 <when value="unpaired">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
136 <param name="unpaired_reads" type="data" format="fastq" label="Unpaired reads" help="FASTQ format" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
137 </when>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
138 <when value="paired-collection">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
139 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastq" collection_type="paired" help="FASTQ format" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
140 </when>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
141 </conditional>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
142 </repeat>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
143
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
144 <!-- PacBio -->
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
145 <repeat name="pacbio" title="PacBio CLR reads">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
146 <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." />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
147 </repeat>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
148 <!-- Nanopore -->
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
149 <repeat name="nanopore" title="Nanopore reads">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
150 <param name="nanopore_reads" type="data" format="fastq" label="Nanopore reads." help="FASTQ format. For Nanopore, use single reads above." />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
151 </repeat>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
152 <!-- Sanger -->
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
153 <repeat name="sanger" title="Sanger reads">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
154 <conditional name="file_type">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
155 <param name="type" type="select" label="Select file format" help="No read correction is done on Sanger reads, no need to provide quality information.">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
156 <option value="fasta">fasta</option>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
157 <option value="fastq">fastq</option>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
158 </param>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
159 <when value="fasta">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
160 <param name="sanger_reads" type="data" format="fasta" label="Sanger reads" help="FASTA format" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
161 </when>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
162 <when value="fastq">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
163 <param name="sanger_reads" type="data" format="fastq" label="Sanger reads" help="FASTQ format" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
164 </when>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
165 </conditional>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
166 </repeat>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
167 <!-- Contigs -->
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
168 <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.">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
169 <conditional name="file_type">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
170 <param name="type" type="select" label="Select file format">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
171 <option value="fasta">fasta</option>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
172 <option value="fastq">fastq</option>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
173 </param>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
174 <when value="fasta">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
175 <param name="trusted_contigs" type="data" format="fasta" label="Trusted contigs" help="FASTA format" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
176 </when>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
177 <when value="fastq">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
178 <param name="trusted_contigs" type="data" format="fastq" label="Trusted contigs" help="FASTQ format" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
179 </when>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
180 </conditional>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
181 </repeat>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
182 <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.">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
183 <conditional name="file_type">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
184 <param name="type" type="select" label="Select file format">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
185 <option value="fasta">fasta</option>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
186 <option value="fastq">fastq</option>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
187 </param>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
188 <when value="fasta">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
189 <param name="untrusted_contigs" type="data" format="fasta" label="Untrusted contigs" help="FASTA format" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
190 </when>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
191 <when value="fastq">
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
192 <param name="untrusted_contigs" type="data" format="fastq" label="Untrusted contigs" help="FASTQ format" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
193 </when>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
194 </conditional>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
195 </repeat>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
196 </inputs>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
197 <outputs>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
198 <data name="out_contigs" format="fasta" label="SPAdes contigs (fasta)" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
199 <data name="out_contig_stats" format="tabular" label="SPAdes contig stats" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
200 <data name="out_scaffolds" format="fasta" label="SPAdes scaffolds (fasta)" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
201 <data name="out_scaffold_stats" format="tabular" label="SPAdes scaffold stats" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
202 <data name="out_log" format="txt" label="SPAdes log" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
203 </outputs>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
204 <tests>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
205 <test>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
206 <param name="sc" value="false" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
207 <param name="careful" value="false" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
208 <param name="kmers" value="33,55" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
209 <param name="lib_type" value="paired_end" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
210 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
211 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
212 <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" />
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
213 </test>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
214 </tests>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
215 <help>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
216 **What it does**
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
217
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
218 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.
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
219
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
220 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.
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
221
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
222 **License**
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
223
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
224 SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2.
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
225
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
226 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.
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
227
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
228 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.
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
229
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
230 You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
231
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
232 ** Acknowledgments **
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
233
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
234 Original wrapper developed by Lionel Guy.
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
235
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
236 Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes.
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
237
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
238 Nicola Soranzo fixed various bugs.
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
239 </help>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
240 <citations>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
241 <citation type="doi">10.1089/cmb.2012.0021</citation>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
242 </citations>
27b90e43e2d8 planemo upload commit 6cd8dfa9e518c63a0b0e3fd5167424cffd3829fc
nml
parents:
diff changeset
243 </tool>