spades: spades.xml annotate

annotate spades.xml @ 3:6dff6ed33cd7 draft

planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753

author	nml
date	Wed, 06 Jul 2016 16:01:02 -0400
parents	e37014a072e9
children	35cb17bd8bf9

rev	line source
3 6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	1 <tool id="spades" name="spades" version="1.3.2">
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 $careful
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	26 -t \${GALAXY_SLOTS:-16}
3 6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	27
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	28 #if str($kmer_choice.auto_kmer_choice) == 'False':
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	29 -k "$kmer_choice.kmers"
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	30 #else
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	31
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	32 #end if
0 009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	33
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	34 #if $cov.state == "auto":
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	35 --cov-cutoff 'auto'
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	36 #elif $cov.state == "value":
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	37 --cov-cutoff '$cov.cutoff'
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	38 #end if
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	39
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	40 $iontorrent
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	41
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	42 ## Sequence files, libraries
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	43 #for $i, $library in enumerate( $libraries )
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	44 #set num=$i+1
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	45 #if str( $library.lib_type ) == "paired_end":
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	46 #set prefix = 'pe'
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	47 #elif str( $library.lib_type ) == "mate_paired":
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	48 #set prefix = 'mp'
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	49 #elif str( $library.lib_type ) == "nxmate_paired":
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	50 #set prefix = 'nxmate'
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	51 #else:
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	52 #set prefix = 'hqmp'
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	53 #end if
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	54 --$prefix$num-$library.orientation
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	55 #for $file in $library.files
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	56 #if $file.file_type.type == "separate"
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	57 --$prefix$num-1 fastq:$file.file_type.fwd_reads
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	58 --$prefix$num-2 fastq:$file.file_type.rev_reads
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	59 #elif $file.file_type.type == "interleaved"
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	60 --$prefix$num-12 fastq:$file.file_type.interleaved_reads
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	61 #elif $file.file_type.type == "unpaired"
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	62 --$prefix$num-s fastq:$file.file_type.unpaired_reads
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	63 #elif $file.file_type.type == "paired-collection"
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	64 --$prefix$num-1 fastq:$file.file_type.fastq_collection.forward
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	65 --$prefix$num-2 fastq:$file.file_type.fastq_collection.reverse
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	66 #end if
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	67 #end for
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	68 #end for
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	69 ## PacBio reads
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	70 #for $i, $pacbiolib in enumerate( $pacbio )
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	71 --pacbio fastq:$pacbiolib.pacbio_reads
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	72 #end for
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	73 ## Nanopore
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	74 #for $i, $nanoporelib in enumerate( $nanopore )
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	75 --nanopore fastq:$nanoporelib.nanopore_reads
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	76 #end for
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	77 ## Sanger
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	78 #for $i, $sangerlib in enumerate( $sanger )
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	79 --sanger $sangerlib.file_type.type:$sangerlib.file_type.sanger_reads
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	80 #end for
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	81 ## Contigs
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	82 #for $i, $trustedcontigs in enumerate( $trustedcontigs )
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	83 --trusted-contigs $trustedcontigs.file_type.type:$trustedcontigs.file_type.trusted_contigs
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	84 #end for
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	85 #for $i, $untrustedcontigs in enumerate( $untrustedcontigs )
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	86 --untrusted-contigs $untrustedcontigs.file_type.type:$untrustedcontigs.file_type.untrusted_contigs
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	87 #end for
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	88 </command>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	89 <inputs>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	90 <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	91 <option value="false">No</option>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	92 <option value="true">Yes</option>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	93 </param>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	94 <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	95 <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)." />
3 6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	96 <conditional name="kmer_choice">
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	97 <param name="auto_kmer_choice" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Automatically choose k-mer values" help="k-mer choices can be chosen by SPAdes instead of being entered manually" />
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	98 <when value="false">
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	99 <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." />
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	100 </when>
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	101 <when value="true"> </when>
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	102 </conditional>
0 009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	103 <conditional name="cov">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	104 <param name="state" type="select" label="Coverage Cutoff">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	105 <option value="off">Off</option>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	106 <option value="value">User Specific</option>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	107 <option value="auto">Auto</option>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	108 </param>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	109 <when value="off">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	110 </when>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	111 <when value="value">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	112 <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	113 </when>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	114 <when value="auto">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	115 </when>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	116 </conditional>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	117
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	118
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	119
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	120 <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	121 <!-- Reads -->
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	122 <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	123 <param name="lib_type" type="select" label="Library type">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	124 <option value="paired_end">Paired-end / Single reads</option>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	125 <option value="mate_paired">Mate pairs</option>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	126 <option value="high_mate_paired">High Quality Mate pairs</option>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	127 <option value="nxmate_paired">Lucigen NxMate pairs</option>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	128 </param>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	129 <param name="orientation" type="select" label="Orientation">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	130 <option value="fr" selected="true">-> <- (fr)</option>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	131 <option value="rf"><- -> (rf)</option>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	132 <option value="ff">-> -> (ff)</option>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	133 </param>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	134 <repeat name="files" title="Files" min="1">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	135 <conditional name="file_type">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	136 <param name="type" type="select" label="Select file format">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	137 <option value="separate">Separate input files</option>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	138 <option value="interleaved">Interleaved files</option>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	139 <option value="unpaired">Unpaired/Single reads</option>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	140 <option value="paired-collection">Paired List Collection</option>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	141 </param>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	142 <when value="separate">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	143 <param name="fwd_reads" type="data" format="fastq" label="Forward reads" help="FASTQ format" />
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	144 <param name="rev_reads" type="data" format="fastq" label="Reverse reads" 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 <when value="interleaved">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	147 <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	148 </when>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	149 <when value="unpaired">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	150 <param name="unpaired_reads" type="data" format="fastq" label="Unpaired reads" help="FASTQ format" />
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	151 </when>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	152 <when value="paired-collection">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	153 <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	154 </when>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	155 </conditional>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	156 </repeat>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	157 </repeat>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	158 <!-- PacBio -->
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	159 <repeat name="pacbio" title="PacBio CLR reads">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	160 <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	161 </repeat>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	162 <!-- Nanopore -->
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	163 <repeat name="nanopore" title="Nanopore reads">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	164 <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	165 </repeat>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	166 <!-- Sanger -->
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	167 <repeat name="sanger" title="Sanger reads">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	168 <conditional name="file_type">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	169 <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	170 <option value="fasta">fasta</option>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	171 <option value="fastq">fastq</option>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	172 </param>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	173 <when value="fasta">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	174 <param name="sanger_reads" type="data" format="fasta" label="Sanger reads" help="FASTA format" />
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	175 </when>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	176 <when value="fastq">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	177 <param name="sanger_reads" type="data" format="fastq" label="Sanger reads" help="FASTQ format" />
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	178 </when>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	179 </conditional>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	180 </repeat>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	181 <!-- Contigs -->
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	182 <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	183 <conditional name="file_type">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	184 <param name="type" type="select" label="Select file format">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	185 <option value="fasta">fasta</option>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	186 <option value="fastq">fastq</option>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	187 </param>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	188 <when value="fasta">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	189 <param name="trusted_contigs" type="data" format="fasta" label="Trusted contigs" help="FASTA format" />
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	190 </when>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	191 <when value="fastq">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	192 <param name="trusted_contigs" type="data" format="fastq" label="Trusted contigs" help="FASTQ format" />
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	193 </when>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	194 </conditional>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	195 </repeat>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	196 <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	197 <conditional name="file_type">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	198 <param name="type" type="select" label="Select file format">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	199 <option value="fasta">fasta</option>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	200 <option value="fastq">fastq</option>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	201 </param>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	202 <when value="fasta">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	203 <param name="untrusted_contigs" type="data" format="fasta" label="Untrusted contigs" help="FASTA format" />
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	204 </when>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	205 <when value="fastq">
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	206 <param name="untrusted_contigs" type="data" format="fastq" label="Untrusted contigs" help="FASTQ format" />
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	207 </when>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	208 </conditional>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	209 </repeat>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	210 </inputs>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	211 <outputs>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	212 <data name="out_contigs" format="fasta" label="SPAdes contigs (fasta)" />
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	213 <data name="out_contig_stats" format="tabular" label="SPAdes contig stats" />
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	214 <data name="out_scaffolds" format="fasta" label="SPAdes scaffolds (fasta)" />
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	215 <data name="out_scaffold_stats" format="tabular" label="SPAdes scaffold stats" />
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	216 <data name="out_log" format="txt" label="SPAdes log" />
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	217 </outputs>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	218 <tests>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	219 <test>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	220 <param name="sc" value="false" />
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	221 <param name="careful" value="false" />
3 6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	222 <param name="kmers" value="33" />
0 009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	223 <param name="lib_type" value="paired_end" />
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	224 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" />
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	225 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
3 6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	226 <output name="out_contigs" file="kmer_33_output.fa" ftype="fasta" compare="re_match" lines_diff="1" />
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	227 </test>
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	228 <test>
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	229 <param name="sc" value="false" />
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	230 <param name="careful" value="false" />
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	231 <param name="auto_kmer_choice" value="true" />
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	232 <param name="lib_type" value="paired_end" />
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	233 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" />
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	234 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	235 <output name="out_contigs" file="auto_kmer_output.fa" ftype="fasta" compare="re_match" lines_diff="1" />
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	236 </test>
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	237 <test>
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	238 <param name="sc" value="false" />
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	239 <param name="careful" value="false" />
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	240 <param name="kmers" value="77" />
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	241 <param name="lib_type" value="paired_end" />
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	242 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" />
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	243 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	244 <output name="out_contigs" file="kmer_77_output.fa" ftype="fasta" compare="re_match" lines_diff="1" />
0 009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	245 </test>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	246 </tests>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	247 <help>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	248 What it does
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	249
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	250 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	251
2 e37014a072e9 planemo upload commit 733f396b6a4397c3b133bcb6fb3c10f5970db230-dirty nml parents: 1 diff changeset	252 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	253
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	254 License
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	255
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	256 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	257
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	258 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	259
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	260 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	261
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	262 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	263
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	264 Acknowledgments
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	265
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	266 Original wrapper developed by Lionel Guy.
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	267
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	268 Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes.
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	269
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	270 Nicola Soranzo fixed various bugs.
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	271 </help>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	272 <citations>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	273 <citation type="doi">10.1089/cmb.2012.0021</citation>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	274 </citations>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	275 </tool>

Mercurial > repos > nml > spades

annotate spades.xml @ 3:6dff6ed33cd7 draft