Mercurial > repos > iuc > unicycler
changeset 2:e92675014ac9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 03633ebc76d814bac6b98298349222b3cf4541cb
| author | iuc |
|---|---|
| date | Tue, 28 Nov 2017 10:53:47 -0500 |
| parents | f13d0498a199 |
| children | c4eac0c7e542 |
| files | unicycler.xml |
| diffstat | 1 files changed, 260 insertions(+), 234 deletions(-) [+] |
line wrap: on
line diff
--- a/unicycler.xml Fri Sep 29 11:03:48 2017 -0400 +++ b/unicycler.xml Tue Nov 28 10:53:47 2017 -0500 @@ -1,188 +1,114 @@ -<tool id="unicycler" name="Create assemblies with Unicycler" version="0.4.1"> +<tool id="unicycler" name="Create assemblies with Unicycler" version="@VERSION@.1"> + <macros> + <token name="@VERSION@">0.4.1</token> + </macros> <requirements> - <requirement type="package" version="0.4.1">unicycler</requirement> + <requirement type="package" version="@VERSION@">unicycler</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - - ## Preparing files - - #if str( $paired_unpaired.fastq_input_selector ) == "paired": - - #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger'): - ln -s '${paired_unpaired.fastq_input1}' fq1.fastq && - #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz'): - ln -s '${paired_unpaired.fastq_input1}' fq1.fastq.gz && - #end if - - #if $paired_unpaired.fastq_input2.is_of_type('fastqsanger'): - ln -s '${paired_unpaired.fastq_input2}' fq2.fastq && - #elif $paired_unpaired.fastq_input2.is_of_type('fastqsanger.gz'): - ln -s '${paired_unpaired.fastq_input1}' fq2.fastq.gz && - #end if - - #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection": - - #if $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger'): - ln -s '${paired_unpaired.fastq_input1.forward}' fq1.fastq && - #elif $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger.gz'): - ln -s '${paired_unpaired.fastq_input1.forward}' fq1.fastq.gz && - #end if - - #if $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger'): - ln -s '${paired_unpaired.fastq_input1.reverse}' fq2.fastq && - #elif $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger.gz'): - ln -s '${paired_unpaired.fastq_input2.reverse}' fq2.fastq.gz && - #end if - - #elif str( $paired_unpaired.fastq_input_selector ) == "single": - - #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger'): - ln -s '${paired_unpaired.fastq_input1}' fq.fastq && - #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz'): - ln -s '${paired_unpaired.fastq_input1}' fq.fastq.gz && - #end if - +## Preparing files +#if str( $paired_unpaired.fastq_input_selector ) == "paired" + #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger') + #set fq1 = "fq1.fastq" + #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz') + #set fq1 = "fq1.fastq.gz" + #end if + #if $paired_unpaired.fastq_input2.is_of_type('fastqsanger') + #set fq2 = "fq2.fastq" + #elif $paired_unpaired.fastq_input2.is_of_type('fastqsanger.gz') + #set fq2 = "fq2.fastq.gz" + #end if + ln -s '${paired_unpaired.fastq_input1}' $fq1 && + ln -s '${paired_unpaired.fastq_input2}' $fq2 && +#elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection" + #if $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger') + #set fq1 = "fq1.fastq" + #elif $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger.gz') + #set fq1 = "fq1.fastq.gz" #end if - - ## Get location for pilon installation - - pilon=`pilon --jar_dir` && - - #if $long_reads: - #if $long_reads.is_of_type('fastqsanger'): - #set lr = "lr.fastq" - ln -s '${long_reads}' lr.fastq && - #elif $long_reads.is_of_type('fastqsanger.gz'): - #set lr = "lr.fastq.gz" - ln -s '${long_reads}' lr.fastq.gz && - #elif $long_reads.is_of_type('fasta'): - #set lr = "lr.fasta" - ln -s '${long_reads}' lr.fasta && - #end if + #if $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger') + #set fq2 = "fq2.fastq" + #elif $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger.gz') + #set fq2 = "fq2.fastq.gz" #end if - - ## Running Unicycler - - unicycler -t "\${GALAXY_SLOTS:-4}" - - -o ./ - --verbosity 3 - --pilon_path \$pilon - - #if str( $paired_unpaired.fastq_input_selector ) != "single": - - #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger'): - -1 fq1.fastq - #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz'): - -1 fq1.fastq.gz - #end if - - #if $paired_unpaired.fastq_input2.is_of_type('fastqsanger'): - -2 fq2.fastq - #elif $paired_unpaired.fastq_input2.is_of_type('fastqsanger.gz'): - -2 fq2.fastq.gz - #end if - - #else: - - #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger'): - -s fq.fastq - #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz'): - -s fq.fastq.gz - #end if - + ln -s '${paired_unpaired.fastq_input1.forward}' $fq1 && + ln -s '${paired_unpaired.fastq_input1.reverse}' $fq2 && +#elif str( $paired_unpaired.fastq_input_selector ) == "single" + #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger') + #set fq = "fq.fastq" + #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz') + #set fq = "fq.fastq.gz" + #end if + ln -s '${paired_unpaired.fastq_input1}' '$fq' && +#end if +#if $long + #if $long.is_of_type('fastqsanger') + #set lr = "lr.fastq" + #elif $long.is_of_type('fastqsanger.gz') + #set lr = "lr.fastq.gz" + #elif $long.is_of_type('fasta') + #set lr = "lr.fasta" #end if - - #if $long_reads: - - -l $lr - - #end if - - ## General Unicycler Options section - ## ---------------------------------------------------------- - - --mode '${uc_opt.mode}' - - #if $uc_opt.min_fasta_length: - --min_fasta_length $uc_opt.min_fasta_length - #end if - - #if $uc_opt.lin_seq: - --expected_linear $uc_opt.lin_seq - #end if - - $uc_opt.no_correct - $uc_opt.no_rotate - - ## Rotation Options section - ## ---------------------------------------------------------- - - #if $spades.min_kmer_frac: - --min_kmer_frac $spades.min_kmer_frac - #end if - - #if $spades.max_kmer_frac: - --max_kmer_frac $spades.max_kmer_frac - #end if - - #if $spades.kmer_count: - --kmer_count $spades.kmer_count - #end if - - ## Rotation Options section - ## ---------------------------------------------------------- - - #if $rotation.start_genes: - --start_genes '${rotation.rotation_fasta.start_genes}' - #end if - - #if $rotation.start_gene_id: - --start_gene_id $rotation.start_gene_id - #end if - - #if $rotation.start_gene_cov: - --start_gene_cov $rotation.start_gene_cov - #end if - - ## Pilon Options section - ## ---------------------------------------------------------- - - #if $pilon.min_polish_size: - --min_polish_size $pilon.min_polish_size - #end if - - ## Graph Cleaning Options sdection - ## ---------------------------------------------------------- - - #if $graph_clean.min_component_size: - --min_component_size $graph_clean.min_component_size - #end if - #if $graph_clean.min_dead_end_size: - --min_dead_end_size $graph_clean.min_dead_end_size - #end if - - ## Long Read Alignment Options - ## ---------------------------------------------------------- - - - #if $lr_align.contamination_fasta: - --contamination '${lr_align.contamination_fasta}' - #end if - - #if $lr_align.scores: - --scores '${lr_align.scores}' - #end if - - #if $lr_align.low_score: - --low_score $lr_align.low_score - #end if - - ## Miniasm requires racon, which is not available for python 3.x - --no_miniasm - + ln -s '${long}' '$lr' && +#end if +## Get location for pilon installation +pilon=`pilon --jar_dir` && +## Running Unicycler +unicycler -t "\${GALAXY_SLOTS:-4}" +-o ./ +--verbosity 3 +--pilon_path \$pilon +#if str( $paired_unpaired.fastq_input_selector ) != "single" + -1 '$fq1' + -2 '$fq2' +#else + -s '$fq' +#end if +#if $long + -l $lr +#end if +## General Unicycler Options section +## ---------------------------------------------------------- +--mode '$mode' +--min_fasta_length '$min_fasta_length' +--linear_seqs '$linear_seqs' +## Spades Options section +## ---------------------------------------------------------- +$spades.no_correct +--min_kmer_frac '$spades.min_kmer_frac' +--max_kmer_frac '$spades.max_kmer_frac' +--kmer_count '$spades.kmer_count' +--depth_filter '$spades.depth_filter' +## Rotation Options section +## ---------------------------------------------------------- +$rotation.no_rotate +#if $rotation.start_genes + --start_genes '$rotation.start_genes' +#end if +--start_gene_id '$rotation.start_gene_id' +--start_gene_cov '$rotation.start_gene_cov' +## Pilon Options section +## ---------------------------------------------------------- +$pilon.no_pilon +#if str($pilon.min_polish_size) != '' + --min_polish_size '$pilon.min_polish_size' +#end if +## Graph cleaning Options sdection +## ---------------------------------------------------------- +--min_component_size '$graph_clean.min_component_size' +--min_dead_end_size '$graph_clean.min_dead_end_size' +## Long Read Alignment Options +## ---------------------------------------------------------- +#if $lr_align.contamination + --contamination '$lr_align.contamination' +#end if +--scores '${lr_align.scores}' +#if str($lr_align.low_score) != '' + --low_score '$lr_align.low_score' +#end if +## Miniasm requires racon, which is not available for python 3.x +--no_miniasm ]]></command> - <inputs> <conditional name="paired_unpaired"> <param name="fastq_input_selector" type="select" label="Paired or Single end data?" help="Select between paired and single end data"> @@ -201,64 +127,84 @@ <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz" label="Select unpaired reads" help="Specify dataset with unpaired reads"/> </when> </conditional> - <param name="long_reads" argument="--long" optional="True" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select long reads. If there are no long reads, leave this empty"/> - - <section name="uc_opt" expanded="True" title="Unicycler options"> - <param argument="--mode" type="select" label="Select Bridging mode"> - <option value="conservative">Conservative (smaller contigs, lower misassembly)</option> - <option value="normal" selected="True">Normal (moderate contig size and misassembly rate)</option> - <option value="bold">Bold (longest contigs, higher misassembly rate)</option> - </param> - <param argument="--min_fasta_length" optional="True" type="integer" value="" label="Exclude contigs from the FASTA file which are shorter than this length (bp)" help="default = 1"/> - <param argument="--no_correct" optional="True" 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."/> - <param argument="--no_rotate" optional="True" 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."/> - <param argument="--no_pilon" optional="True" 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."/> - <param name="lin_seq" argument="--expected_linear_seqs" optional="True" type="integer" value="" label="The expected number of linear (i.e. non-circular) sequences in the assembly" help="default = 0"/> - </section> - + <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"/> + <param argument="--mode" type="select" label="Select Bridging mode"> + <option value="conservative">Conservative (smaller contigs, lower misassembly)</option> + <option value="normal" selected="True">Normal (moderate contig size and misassembly rate)</option> + <option value="bold">Bold (longest contigs, higher misassembly rate)</option> + </param> + <param argument="--min_fasta_length" type="integer" value="100" label="Exclude contigs from the FASTA file which are shorter than this length (bp)"/> + <param argument="--linear_seqs" type="integer" value="0" label="The expected number of linear (i.e. non-circular) sequences in the assembly"/> <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!"> - <param argument="--min_kmer_frac" optional="True" type="float" min="0" max="1" value="" label="Lowest k-mer size for SPAdes assembly, expressed as a fraction of the read length" help="default = 0.2"/> - <param argument="--max_kmer_frac" optional="True" type="float" min="0" max="1" value="" label="Highest k-mer size for SPAdes assembly, expressed as a fraction of the read length" help="default = 0.95"/> - <param argument="--kmer_count" optional="True" type="integer" value="" label="Number of k-mer steps to use in SPAdes assembly" help="default = 10"/> + <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."/> + <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"/> + <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"/> + <param argument="--kmer_count" type="integer" min="0" value="10" label="Number of k-mer steps to use in SPAdes assembly"/> + <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"/> </section> - - <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!"> - <param argument="--start_genes" optional="True" type="data" format="fasta" label="FASTA file of genes for start point of rotated replicons" /> - <param argument="--start_gene_id" optional="True" type="integer" min="0" max="100" value="" label="The minimum required BLAST percent identity for a start gene search" help="default = 90"/> - <param argument="--start_gene_cov" optional="True" type="integer" min="0" max="100" value="" label="The minimum required BLAST percent coverage for a start gene search" help="default = 95"/> - </section> - - <section name="pilon" title="Pilon options" expanded="False"> - <param argument="--min_polish_size" optional="True" type="integer" min="0" label="Contigs shorter than this value (bp) will not be polished using Pilon" help="default = 1000"/> + <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!"> + <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."/> + <param argument="--start_genes" optional="true" type="data" format="fasta" label="FASTA file of genes for start point of rotated replicons" /> + <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"/> + <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"/> </section> - - <section name="graph_clean" expanded="False" title="Graph cleaning options" help="These options control the removal of small leftover sequences after bridging is complete."> - <param argument="--min_component_size" optional="True" type="integer" value="" label="Unbridged graph components smaller than this size will be removed from the final graph" help="default = 1000"/> - <param argument="--min_dead_end_size" optional="True" type="integer" value="" label="Graph dead ends smaller than this size will be removed from the final graph" help="default = 1000"/> + <section name="pilon" title="Pilon options" expanded="false"> + <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."/> + <param argument="--min_polish_size" type="integer" min="0" value="1000" label="Contigs shorter than this value (bp) will not be polished using Pilon"/> </section> - - <section name="lr_align" expanded="False" title="Long read alignment parameters" help="These options control the alignment of long reads to the assembly graph."> - <param name="contamination_fasta" 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." /> - <param argument="--scores" optional="True" type="text" value="" label="Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend" help="default = 3,-6,-5,-2"/> - <param argument="--low_score" optional="True" type="integer" value="" label="Score threshold - alignments below this are considered poor" help="default = set automatically"/> + <section name="graph_clean" expanded="false" title="Graph cleaning options" help="These options control the removal of small leftover sequences after bridging is complete."> + <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" /> + <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"/> + </section> + <section name="lr_align" expanded="false" title="Long read alignment parameters" help="These options control the alignment of long reads to the assembly graph."> + <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." /> + <param argument="--scores" type="text" value="3,-6,-5,-2" label="Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend"/> + <param argument="--low_score" optional="true" type="integer" value="" label="Score threshold - alignments below this are considered poor" help="default = set automatically"/> </section> </inputs> - <outputs> - <data format="txt" name="assembly_grapth" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" /> - <data format="fasta" name="assembly" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/> + <data name="assembly_graph" format="txt" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" /> + <data name="assembly" format="fasta" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/> </outputs> - <tests> <test> - <param name="fastq_input_selector" value="paired" /> - <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" /> - <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" /> + <conditional name="paired_unpaired"> + <param name="fastq_input_selector" value="paired" /> + <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" /> + <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" /> + </conditional> <param name="mode" value="normal" /> - <param name="no_correct" value="true" /> - <param name="no_rotate" value="false" /> - <param name="no_pilon" value="false" /> - <output ftype="fasta" name="assembly"> + <param name="min_fasta_length" value="100"/> + <param name="linear_seqs" value="0"/> + <section name="spades"> + <param name="no_correct" value="true"/> + <param name="min_kmer_frac" value="0.2"/> + <param name="max_kmer_frac" value="0.95"/> + <param name="kmer_count" value="10"/> + <param name="depth_filter" value="0.25"/> + </section> + <section name="rotation"> + <param name="no_rotate" value=""/> + <param name="start_gene_id" value="90"/> + <param name="start_gene_cov" value="95"/> + </section> + <section name="pilon"> + <param name="no_pilon" value=""/> + <param name="min_polish_size" value="1000"/> + </section> + <section name="graph_clean"> + <param name="min_component_size" value="1000"/> + <param name="min_dead_end_size" value="1000"/> + </section> + <section name="lr_align"> + <param name="scores" value="3,-6,-5,-2"/> + </section> + <output name="assembly_graph" ftype="txt"> + <assert_contents> + <has_text text="TACGGGGAAGGACGTC"/> + </assert_contents> + </output> + <output name="assembly" ftype="fasta"> <assert_contents> <has_text text="length=5386" /> </assert_contents> @@ -276,15 +222,91 @@ at: https://gist.github.com/jmchilton/b411b695170c1daea6589f5d76e326cb. --> <test> - <param name="fastq_input_selector" value="paired" /> - <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" /> - <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" /> - <param name="long_reads" value="onp.fa" ftype="fasta" /> + <conditional name="paired_unpaired"> + <param name="fastq_input_selector" value="paired" /> + <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger.gz" /> + <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger.gz" /> + </conditional> + <param name="long" value="onp.fa" ftype="fasta" /> <param name="mode" value="normal" /> - <param name="no_correct" value="true" /> - <param name="no_rotate" value="false" /> - <param name="no_pilon" value="false" /> - <output ftype="fasta" name="assembly"> + <param name="min_fasta_length" value="100"/> + <param name="linear_seqs" value="0"/> + <section name="spades"> + <param name="no_correct" value="true"/> + <param name="min_kmer_frac" value="0.2"/> + <param name="max_kmer_frac" value="0.95"/> + <param name="kmer_count" value="10"/> + <param name="depth_filter" value="0.25"/> + </section> + <section name="rotation"> + <param name="no_rotate" value=""/> + <param name="start_gene_id" value="90"/> + <param name="start_gene_cov" value="95"/> + </section> + <section name="pilon"> + <param name="no_pilon" value=""/> + <param name="min_polish_size" value="1000"/> + </section> + <section name="graph_clean"> + <param name="min_component_size" value="1000"/> + <param name="min_dead_end_size" value="1000"/> + </section> + <section name="lr_align"> + <param name="scores" value="3,-6,-5,-2"/> + </section> + <output name="assembly_graph" ftype="txt"> + <assert_contents> + <has_text text="TACGGGGAAGGACGTC" /> + </assert_contents> + </output> + <output name="assembly" ftype="fasta"> + <assert_contents> + <has_text text="length=5386" /> + </assert_contents> + </output> + </test> + <test> + <conditional name="paired_unpaired"> + <param name="fastq_input_selector" value="paired_collection"/> + <param name="fastq_input1"> + <collection type="paired"> + <element name="forward" value="phix_f.fq.gz" ftype="fastqsanger" /> + <element name="reverse" value="phix_r.fq.gz" ftype="fastqsanger" /> + </collection> + </param> + </conditional> + <param name="mode" value="normal" /> + <param name="min_fasta_length" value="100"/> + <param name="linear_seqs" value="0"/> + <section name="spades"> + <param name="no_correct" value="true"/> + <param name="min_kmer_frac" value="0.2"/> + <param name="max_kmer_frac" value="0.95"/> + <param name="kmer_count" value="10"/> + <param name="depth_filter" value="0.25"/> + </section> + <section name="rotation"> + <param name="no_rotate" value=""/> + <param name="start_gene_id" value="90"/> + <param name="start_gene_cov" value="95"/> + </section> + <section name="pilon"> + <param name="no_pilon" value="true"/> + <param name="min_polish_size" value="1000"/> + </section> + <section name="graph_clean"> + <param name="min_component_size" value="1000"/> + <param name="min_dead_end_size" value="1000"/> + </section> + <section name="lr_align"> + <param name="scores" value="3,-6,-5,-2"/> + </section> + <output name="assembly_graph" ftype="txt"> + <assert_contents> + <has_text text="TACGGGGAAGGACGTC" /> + </assert_contents> + </output> + <output name="assembly" ftype="fasta"> <assert_contents> <has_text text="length=5386" /> </assert_contents> @@ -390,7 +412,7 @@ If you expect your sample to contain linear (non circular) sequences, set this option:: - --expected_linear_seqs EXPECTED_LINEAR_SEQS + --linear_seqs EXPECTED_LINEAR_SEQS The expected number of linear (i.e. non-circular) sequences in the underlying sequence @@ -411,6 +433,10 @@ --kmer_count KMER_COUNT Number of k-mer steps to use in SPAdes assembly (default: 10) + --depth_filter DEPTH_FILTER + Filter out contigs lower than this fraction + of the chromosomal depth, if doing so does + not result in graph dead ends (default: 0.25) ----