unicycler: unicycler.xml annotate

annotate unicycler.xml @ 2:6710edf12bac draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb

author	iuc
date	Tue, 28 Nov 2017 10:53:27 -0500
parents	3c7b8504e32a
children	68779cb38c3a

rev	line source
2 6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	1 <tool id="unicycler" name="Create assemblies with Unicycler" version="@VERSION@.1">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	2 <macros>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	3 <token name="@VERSION@">0.4.1</token>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	4 </macros>
0 15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	5 <requirements>
2 6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	6 <requirement type="package" version="@VERSION@">unicycler</requirement>
0 15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	7 </requirements>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	8 <command detect_errors="exit_code"><![CDATA[
2 6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	9 ## Preparing files
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	10 #if str( $paired_unpaired.fastq_input_selector ) == "paired"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	11 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	12 #set fq1 = "fq1.fastq"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	13 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	14 #set fq1 = "fq1.fastq.gz"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	15 #end if
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	16 #if $paired_unpaired.fastq_input2.is_of_type('fastqsanger')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	17 #set fq2 = "fq2.fastq"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	18 #elif $paired_unpaired.fastq_input2.is_of_type('fastqsanger.gz')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	19 #set fq2 = "fq2.fastq.gz"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	20 #end if
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	21 ln -s '${paired_unpaired.fastq_input1}' $fq1 &&
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	22 ln -s '${paired_unpaired.fastq_input2}' $fq2 &&
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	23 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	24 #if $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	25 #set fq1 = "fq1.fastq"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	26 #elif $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger.gz')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	27 #set fq1 = "fq1.fastq.gz"
0 15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	28 #end if
2 6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	29 #if $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	30 #set fq2 = "fq2.fastq"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	31 #elif $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger.gz')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	32 #set fq2 = "fq2.fastq.gz"
0 15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	33 #end if
2 6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	34 ln -s '${paired_unpaired.fastq_input1.forward}' $fq1 &&
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	35 ln -s '${paired_unpaired.fastq_input1.reverse}' $fq2 &&
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	36 #elif str( $paired_unpaired.fastq_input_selector ) == "single"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	37 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	38 #set fq = "fq.fastq"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	39 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	40 #set fq = "fq.fastq.gz"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	41 #end if
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	42 ln -s '${paired_unpaired.fastq_input1}' '$fq' &&
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	43 #end if
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	44 #if $long
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	45 #if $long.is_of_type('fastqsanger')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	46 #set lr = "lr.fastq"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	47 #elif $long.is_of_type('fastqsanger.gz')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	48 #set lr = "lr.fastq.gz"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	49 #elif $long.is_of_type('fasta')
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	50 #set lr = "lr.fasta"
0 15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	51 #end if
2 6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	52 ln -s '${long}' '$lr' &&
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	53 #end if
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	54 ## Get location for pilon installation
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	55 pilon=`pilon --jar_dir` &&
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	56 ## Running Unicycler
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	57 unicycler -t "\${GALAXY_SLOTS:-4}"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	58 -o ./
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	59 --verbosity 3
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	60 --pilon_path \$pilon
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	61 #if str( $paired_unpaired.fastq_input_selector ) != "single"
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	62 -1 '$fq1'
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	63 -2 '$fq2'
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	64 #else
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	65 -s '$fq'
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	66 #end if
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	67 #if $long
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	68 -l $lr
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	69 #end if
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	70 ## General Unicycler Options section
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	71 ## ----------------------------------------------------------
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	72 --mode '$mode'
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	73 --min_fasta_length '$min_fasta_length'
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	74 --linear_seqs '$linear_seqs'
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	75 ## Spades Options section
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	76 ## ----------------------------------------------------------
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	77 $spades.no_correct
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	78 --min_kmer_frac '$spades.min_kmer_frac'
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	79 --max_kmer_frac '$spades.max_kmer_frac'
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	80 --kmer_count '$spades.kmer_count'
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	81 --depth_filter '$spades.depth_filter'
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	82 ## Rotation Options section
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	83 ## ----------------------------------------------------------
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	84 $rotation.no_rotate
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	85 #if $rotation.start_genes
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	86 --start_genes '$rotation.start_genes'
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	87 #end if
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	88 --start_gene_id '$rotation.start_gene_id'
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	89 --start_gene_cov '$rotation.start_gene_cov'
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	90 ## Pilon Options section
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	91 ## ----------------------------------------------------------
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	92 $pilon.no_pilon
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	93 #if str($pilon.min_polish_size) != ''
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	94 --min_polish_size '$pilon.min_polish_size'
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	95 #end if
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	96 ## Graph cleaning Options sdection
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	97 ## ----------------------------------------------------------
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	98 --min_component_size '$graph_clean.min_component_size'
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	99 --min_dead_end_size '$graph_clean.min_dead_end_size'
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	100 ## Long Read Alignment Options
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	101 ## ----------------------------------------------------------
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	102 #if $lr_align.contamination
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	103 --contamination '$lr_align.contamination'
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	104 #end if
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	105 --scores '${lr_align.scores}'
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	106 #if str($lr_align.low_score) != ''
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	107 --low_score '$lr_align.low_score'
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	108 #end if
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	109 ## Miniasm requires racon, which is not available for python 3.x
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	110 --no_miniasm
0 15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	111 ]]></command>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	112 <inputs>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	113 <conditional name="paired_unpaired">
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	114 <param name="fastq_input_selector" type="select" label="Paired or Single end data?" help="Select between paired and single end data">
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	115 <option selected="True" value="paired">Paired</option>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	116 <option value="paired_collection">Paired Collection</option>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	117 <option value="single">Single</option>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	118 </param>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	119 <when value="paired">
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	120 <param name="fastq_input1" argument="-1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	121 <param name="fastq_input2" argument="-2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	122 </when>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	123 <when value="paired_collection">
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	124 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" />
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	125 </when>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	126 <when value="single">
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	127 <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz" label="Select unpaired reads" help="Specify dataset with unpaired reads"/>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	128 </when>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	129 </conditional>
2 6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	130 <param argument="--long" optional="true" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select long reads. If there are no long reads, leave this empty"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	131 <param argument="--mode" type="select" label="Select Bridging mode">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	132 <option value="conservative">Conservative (smaller contigs, lower misassembly)</option>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	133 <option value="normal" selected="True">Normal (moderate contig size and misassembly rate)</option>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	134 <option value="bold">Bold (longest contigs, higher misassembly rate)</option>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	135 </param>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	136 <param argument="--min_fasta_length" type="integer" value="100" label="Exclude contigs from the FASTA file which are shorter than this length (bp)"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	137 <param argument="--linear_seqs" type="integer" value="0" label="The expected number of linear (i.e. non-circular) sequences in the assembly"/>
0 15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	138 <section name="spades" expanded="False" title="SPAdes options" help="Unicycler uses SPAdes to construct assembly graphs. You can modify some of the SPAdes settings here. Use this ONLY if you know what you are doing!">
2 6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	139 <param argument="--no_correct" type="boolean" checked="false" truevalue="--no_correct" falsevalue="" label="Skip SPAdes error correction step" help="This option turns off SPAdes error correction. Generally it is highly recommended to use correction."/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	140 <param argument="--min_kmer_frac" type="float" min="0" max="1" value="0.2" label="Lowest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	141 <param argument="--max_kmer_frac" type="float" min="0" max="1" value="0.95" label="Highest k-mer size for SPAdes assembly, expressed as a fraction of the read length"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	142 <param argument="--kmer_count" type="integer" min="0" value="10" label="Number of k-mer steps to use in SPAdes assembly"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	143 <param argument="--depth_filter" type="float" min="0" max="1" value="0.25" label="Filter out contigs lower than this fraction of the chromosomal depth" help="It is done if does not result in graph dead ends"/>
0 15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	144 </section>
2 6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	145 <section name="rotation" expanded="false" title="Rotation options" help="These options control the rotation of completed circular sequence near the end of the Unicycler pipeline. Use this ONLY if you know what you are doing!">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	146 <param argument="--no_rotate" type="boolean" checked="false" truevalue="--no_rotate" falsevalue="" label="Do not rotate completed replicons to start at a standard gene." help="Unicycler uses TBLASTN to search for dnaA or repA alleles in each completed replicon. If one is found, the sequence is rotated and/or flipped so that it begins with that gene encoded on the forward strand. This provides consistently oriented assemblies and reduces the risk that a gene will be split across the start and end of the sequence."/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	147 <param argument="--start_genes" optional="true" type="data" format="fasta" label="FASTA file of genes for start point of rotated replicons" />
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	148 <param argument="--start_gene_id" type="float" min="0" max="100" value="90" label="The minimum required BLAST percent identity for a start gene search"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	149 <param argument="--start_gene_cov" type="float" min="0" max="100" value="95" label="The minimum required BLAST percent coverage for a start gene search"/>
0 15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	150 </section>
2 6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	151 <section name="pilon" title="Pilon options" expanded="false">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	152 <param argument="--no_pilon" type="boolean" checked="false" truevalue="--no_pilon" falsevalue="" label="Do not use Pilon to polish the final assembly." help="Unicycler uses Pilon tool for polishing final assembly."/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	153 <param argument="--min_polish_size" type="integer" min="0" value="1000" label="Contigs shorter than this value (bp) will not be polished using Pilon"/>
0 15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	154 </section>
2 6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	155 <section name="graph_clean" expanded="false" title="Graph cleaning options" help="These options control the removal of small leftover sequences after bridging is complete.">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	156 <param argument="--min_component_size" type="integer" min="0" value="1000" label="Unbridged graph components smaller than this size will be removed from the final graph" />
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	157 <param argument="--min_dead_end_size" type="integer" min="0" value="1000" label="Graph dead ends smaller than this size will be removed from the final graph"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	158 </section>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	159 <section name="lr_align" expanded="false" title="Long read alignment parameters" help="These options control the alignment of long reads to the assembly graph.">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	160 <param argument="--contamination" optional="true" type="data" format="fasta" label="FASTA file of known contamination in long reads, e.g. lambda, phiXm or puc18 spike-ins." />
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	161 <param argument="--scores" type="text" value="3,-6,-5,-2" label="Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	162 <param argument="--low_score" optional="true" type="integer" value="" label="Score threshold - alignments below this are considered poor" help="default = set automatically"/>
0 15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	163 </section>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	164 </inputs>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	165 <outputs>
2 6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	166 <data name="assembly_graph" format="txt" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" />
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	167 <data name="assembly" format="fasta" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/>
0 15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	168 </outputs>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	169 <tests>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	170 <test>
2 6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	171 <conditional name="paired_unpaired">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	172 <param name="fastq_input_selector" value="paired" />
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	173 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" />
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	174 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" />
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	175 </conditional>
0 15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	176 <param name="mode" value="normal" />
2 6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	177 <param name="min_fasta_length" value="100"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	178 <param name="linear_seqs" value="0"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	179 <section name="spades">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	180 <param name="no_correct" value="true"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	181 <param name="min_kmer_frac" value="0.2"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	182 <param name="max_kmer_frac" value="0.95"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	183 <param name="kmer_count" value="10"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	184 <param name="depth_filter" value="0.25"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	185 </section>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	186 <section name="rotation">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	187 <param name="no_rotate" value=""/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	188 <param name="start_gene_id" value="90"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	189 <param name="start_gene_cov" value="95"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	190 </section>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	191 <section name="pilon">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	192 <param name="no_pilon" value=""/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	193 <param name="min_polish_size" value="1000"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	194 </section>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	195 <section name="graph_clean">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	196 <param name="min_component_size" value="1000"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	197 <param name="min_dead_end_size" value="1000"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	198 </section>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	199 <section name="lr_align">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	200 <param name="scores" value="3,-6,-5,-2"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	201 </section>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	202 <output name="assembly_graph" ftype="txt">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	203 <assert_contents>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	204 <has_text text="TACGGGGAAGGACGTC"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	205 </assert_contents>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	206 </output>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	207 <output name="assembly" ftype="fasta">
0 15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	208 <assert_contents>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	209 <has_text text="length=5386" />
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	210 </assert_contents>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	211 </output>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	212 </test>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	213 <!--
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	214 Following test corresponds to the command:
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	215
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	216 unicycler -t "${GALAXY_SLOTS:-8}" -o ./ - -verbose 3 - -pilon_path `pilon - -jar_dir` \
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	217 -1 test-data/phix_f.fq.gz -2 test-data/phix_r.fq.gz -l test-data/onp.fa \
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	218 - -mode 'normal' - -no_correct
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	219
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	220 This command causes a segfault with the current version of unicycler on bioconda for Linux
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	221 during the minimap step (which seems to be compiled C code). A gist of the log can be found
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	222 at: https://gist.github.com/jmchilton/b411b695170c1daea6589f5d76e326cb.
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	223 -->
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	224 <test>
2 6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	225 <conditional name="paired_unpaired">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	226 <param name="fastq_input_selector" value="paired" />
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	227 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger.gz" />
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	228 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger.gz" />
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	229 </conditional>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	230 <param name="long" value="onp.fa" ftype="fasta" />
0 15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	231 <param name="mode" value="normal" />
2 6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	232 <param name="min_fasta_length" value="100"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	233 <param name="linear_seqs" value="0"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	234 <section name="spades">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	235 <param name="no_correct" value="true"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	236 <param name="min_kmer_frac" value="0.2"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	237 <param name="max_kmer_frac" value="0.95"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	238 <param name="kmer_count" value="10"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	239 <param name="depth_filter" value="0.25"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	240 </section>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	241 <section name="rotation">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	242 <param name="no_rotate" value=""/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	243 <param name="start_gene_id" value="90"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	244 <param name="start_gene_cov" value="95"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	245 </section>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	246 <section name="pilon">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	247 <param name="no_pilon" value=""/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	248 <param name="min_polish_size" value="1000"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	249 </section>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	250 <section name="graph_clean">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	251 <param name="min_component_size" value="1000"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	252 <param name="min_dead_end_size" value="1000"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	253 </section>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	254 <section name="lr_align">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	255 <param name="scores" value="3,-6,-5,-2"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	256 </section>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	257 <output name="assembly_graph" ftype="txt">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	258 <assert_contents>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	259 <has_text text="TACGGGGAAGGACGTC" />
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	260 </assert_contents>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	261 </output>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	262 <output name="assembly" ftype="fasta">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	263 <assert_contents>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	264 <has_text text="length=5386" />
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	265 </assert_contents>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	266 </output>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	267 </test>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	268 <test>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	269 <conditional name="paired_unpaired">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	270 <param name="fastq_input_selector" value="paired_collection"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	271 <param name="fastq_input1">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	272 <collection type="paired">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	273 <element name="forward" value="phix_f.fq.gz" ftype="fastqsanger" />
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	274 <element name="reverse" value="phix_r.fq.gz" ftype="fastqsanger" />
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	275 </collection>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	276 </param>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	277 </conditional>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	278 <param name="mode" value="normal" />
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	279 <param name="min_fasta_length" value="100"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	280 <param name="linear_seqs" value="0"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	281 <section name="spades">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	282 <param name="no_correct" value="true"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	283 <param name="min_kmer_frac" value="0.2"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	284 <param name="max_kmer_frac" value="0.95"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	285 <param name="kmer_count" value="10"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	286 <param name="depth_filter" value="0.25"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	287 </section>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	288 <section name="rotation">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	289 <param name="no_rotate" value=""/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	290 <param name="start_gene_id" value="90"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	291 <param name="start_gene_cov" value="95"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	292 </section>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	293 <section name="pilon">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	294 <param name="no_pilon" value="true"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	295 <param name="min_polish_size" value="1000"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	296 </section>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	297 <section name="graph_clean">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	298 <param name="min_component_size" value="1000"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	299 <param name="min_dead_end_size" value="1000"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	300 </section>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	301 <section name="lr_align">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	302 <param name="scores" value="3,-6,-5,-2"/>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	303 </section>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	304 <output name="assembly_graph" ftype="txt">
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	305 <assert_contents>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	306 <has_text text="TACGGGGAAGGACGTC" />
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	307 </assert_contents>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	308 </output>
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	309 <output name="assembly" ftype="fasta">
0 15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	310 <assert_contents>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	311 <has_text text="length=5386" />
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	312 </assert_contents>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	313 </output>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	314 </test>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	315 </tests>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	316 <help><![CDATA[
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	317
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	318 Unicycler
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	319
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	320 Unicycler is a hybrid assembly pipeline for bacterial genomes. It uses both Illumina reads and long reads (PacBio or Nanopore) to produce complete and accurate assemblies. It is written by `Ryan Wick`_ at the University of Melbourne's Centre for Systems Genomics. Much of the description below is lifted from Unicycler's `github page`_.
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	321
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	322 .. _`Ryan Wick`: https://github.com/rrwick
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	323 .. _`github page`: https://github.com/rrwick/Unicycler
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	324
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	325 -----
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	326
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	327 Input data
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	328
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	329 Unicycler accepts inputs short (Illumina) reads in FASTQ format. Galaxy places additional requirement of having these in FASTQ format with `Sanger encoding`_ of quality scores. Long reads (from Oxford Nanopore or PacBio) can be either in FASTQ of FASTA form.
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	330
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	331 .. _`Sanger encoding`: https://en.wikipedia.org/wiki/FASTQ_format#Quality
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	332
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	333 The input options are::
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	334
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	335 -1 SHORT1, --short1 SHORT1
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	336 FASTQ file of short reads (first reads in each pair)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	337 -2 SHORT2, --short2 SHORT2
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	338 FASTQ file of short reads (second reads in each pair)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	339 -s SHORT_UNPAIRED, --short_unpaired SHORT_UNPAIRED
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	340 FASTQ file of unpaired short reads
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	341 -l LONG, --long LONG
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	342 FASTQ or FASTA file of long reads, if all reads are available at start.
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	343
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	344 -----
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	345
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	346 Bridging mode
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	347
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	348 Unicycler can be run in three modes: conservative, normal (the default) and bold, set with the --mode option. Conservative mode is least likely to produce a complete assembly but has a very low risk of misassembly. Bold mode is most likely to produce a complete assembly but carries greater risk of misassembly. Normal mode is intermediate regarding both completeness and misassembly risk. See `description of modes`_ for more information.
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	349
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	350 .. _`description of modes`: https://github.com/rrwick/Unicycler#conservative-normal-and-bold
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	351
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	352 The available modes are::
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	353
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	354 --mode {conservative,normal,bold}
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	355 Bridging mode (default: normal)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	356 conservative = smaller contigs, lowest misassembly rate
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	357 normal = moderate contig size and misassembly rate
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	358 bold = longest contigs, higher misassembly rate
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	359
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	360 ----
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	361
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	362 Skip SPAdes error correction step
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	363
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	364 Sequencing data contains a substantial number of sequencing errors that manifest themselves as deviations (bulges and non-connected components) within the assembly graph. One of the ways to improve the graph even constructing it is to minimize the amount sequencing errors by performing error correction. SPAdes, which is used by Unicycler for error correction and assembly, uses `BayesHammer`_ to correct the reads. Here is a brief summary of what it does:
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	365
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	366 1. SPAdes (or rather BayesHammer) counts k-mers in reads and computed k-mer statistics that takes into account base quality values.
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	367 2. `Hamming graph`_ is constructed for k-mers is which k-mers are nodes. In this graph edges connect nodes (k-mers) is they differ from each other by a number of nucleotides up to a certain threshold (the `Hamming distance`_). The graph is central to the error correction algorithm.
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	368 3. At this step Bayesian subclustering of the graph produced in the previous step. For each k-mer we now know the center of its subcluster.
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	369 4. Solid k-mers are derived from cluster centers and are assumed to be error free.
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	370 5. Solid k-mers are mapped back to the reads and used to correct them.
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	371
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	372 This step takes considerable time, so if one need to quickly evaluate assemblies this step can be skipped. However, this is not recommended if one if trying to produce a final high quality assembly.
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	373
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	374 .. _`BayesHammer`: https://goo.gl/1iGkMe
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	375 .. _`Hamming graph`: https://en.wikipedia.org/wiki/Hamming_graph
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	376 .. _`Hamming distance`: https://en.wikipedia.org/wiki/Hamming_distance
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	377
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	378 This following option turns error correction on and off::
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	379
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	380 --no_correct
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	381 Skip SPAdes error correction step
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	382 (default: conduct SPAdes error correction)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	383
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	384 -----
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	385
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	386 Do not rotate completed replicons to start at a standard gene
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	387
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	388 Unicycler uses TBLASTN to search for dnaA or repA alleles in each completed replicon. If one is found, the sequence is rotated and/or flipped so that it begins with that gene encoded on the forward strand. This provides consistently oriented assemblies and reduces the risk that a gene will be split across the start and end of the sequence.
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	389
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	390 The following option turns rotation on and off::
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	391
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	392 --no_rotate
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	393 Do not rotate completed replicons
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	394 to start at a standard gene
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	395 (default: completed replicons are rotated)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	396
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	397 Do not use Pilon to polish the final assembly
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	398
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	399 `Pilon`_ is a tool for improving overall quality of draft assemblies and finding variation among strains. Unicycler uses it for assembly polishing.
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	400
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	401 The following option turns pilon part of Unicycler pipeline on and off::
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	402
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	403 --no_pilon
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	404 Do not use Pilon to polish the
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	405 final assembly (default: Pilon is used)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	406
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	407 .. _`Pilon`: https://github.com/broadinstitute/pilon/wiki
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	408
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	409 ------
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	410
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	411 Expected number of linear sequences
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	412
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	413 If you expect your sample to contain linear (non circular) sequences, set this option::
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	414
2 6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	415 --linear_seqs EXPECTED_LINEAR_SEQS
0 15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	416 The expected number of linear (i.e. non-circular)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	417 sequences in the underlying sequence
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	418
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	419 ----
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	420
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	421 SPAdes options
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	422
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	423 This section provides control of SPAdes options::
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	424
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	425 --min_kmer_frac MIN_KMER_FRAC
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	426 Lowest k-mer size for SPAdes assembly,
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	427 expressed as a fraction of the read length
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	428 (default: 0.2)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	429 --max_kmer_frac MAX_KMER_FRAC
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	430 Highest k-mer size for SPAdes assembly,
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	431 expressed as a fraction of the read length
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	432 (default: 0.95)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	433 --kmer_count KMER_COUNT
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	434 Number of k-mer steps to use in
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	435 SPAdes assembly (default: 10)
2 6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	436 --depth_filter DEPTH_FILTER
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	437 Filter out contigs lower than this fraction
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	438 of the chromosomal depth, if doing so does
6710edf12bac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb iuc parents: 1 diff changeset	439 not result in graph dead ends (default: 0.25)
0 15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	440
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	441 ----
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	442
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	443 Rotation options
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	444
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	445 Unicycler attempts to rotate circular assemblies to make sure that they begin at a consistent starting gene. The following parameters control assembly rotation::
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	446
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	447 --start_genes START_GENES
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	448 FASTA file of genes for start point
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	449 of rotated replicons
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	450 (default: start_genes.fasta)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	451 --start_gene_id START_GENE_ID
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	452 The minimum required BLAST percent identity
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	453 for a start gene search
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	454 (default: 90.0)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	455 --start_gene_cov START_GENE_COV
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	456 The minimum required BLAST percent coverage
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	457 for a start gene search
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	458 (default: 95.0)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	459
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	460 -----
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	461
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	462 Graph cleaning options
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	463
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	464 These options control the removal of small leftover sequences after bridging is complete::
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	465
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	466 --min_component_size MIN_COMPONENT_SIZE
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	467 Unbridged graph components smaller
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	468 than this size (bp) will be removed
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	469 from the final graph (default: 1000)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	470 --min_dead_end_size MIN_DEAD_END_SIZE
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	471 Graph dead ends smaller than this size (bp)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	472 will be removed from the final graph
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	473 (default: 1000)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	474
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	475 -----
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	476
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	477 Long read alignment options
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	478
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	479 These options control the alignment of long reads to the assembly graph::
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	480
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	481 --contamination CONTAMINATION
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	482 FASTA file of known contamination in long reads
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	483 --scores SCORES
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	484 Comma-delimited string of alignment scores:
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	485 match, mismatch, gap open, gap extend
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	486 (default: 3,-6,-5,-2)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	487 --low_score LOW_SCORE
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	488 Score threshold - alignments below this
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	489 are considered poor
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	490 (default: set threshold automatically)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	491
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	492 -----
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	493
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	494 Outputs
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	495
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	496 Galaxy's wrapped for Unicycler produces two outputs:
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	497
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	498 * final assembly in FASTA format
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	499 * final assembly grapth in graph format
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	500
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	501 While most will likely be interested in the FASTA dataset, the graph dataset is also quite useful and can be visualized using tools such as `Bandage`_.
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	502
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	503
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	504 .. _`Bandage`: https://github.com/rrwick/Bandage
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	505
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	506
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	507 ]]></help>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	508 <citations>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	509 <citation type="doi">10.1101/096412</citation>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	510 </citations>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b iuc parents: diff changeset	511 </tool>

Mercurial > repos > iuc > unicycler

annotate unicycler.xml @ 2:6710edf12bac draft