Mercurial > repos > bgruening > nextdenovo
changeset 0:733eab97b979 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo commit 5890a5b5b51cfe2dc4a1bbe1866ce508a9f9ce9f
| author | bgruening |
|---|---|
| date | Thu, 09 Feb 2023 21:24:58 +0000 |
| parents | |
| children | |
| files | macros.xml nextdenovo.xml test-data/nanopore.fasta.gz |
| diffstat | 3 files changed, 247 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Feb 09 21:24:58 2023 +0000 @@ -0,0 +1,27 @@ +<macros> + <token name="@TOOL_VERSION@">2.5.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">nextdenovo</requirement> + </requirements> + </xml> + <xml name="biotools"> + <xrefs> + <xref type="bio.tools">nextdenovo</xref> + </xrefs> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{githubNextDenovo, + author = {Jiang, Hu}, + year = {2022}, + title = {NextDenovo}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/Nextomics/NextDenovo}} + </citation> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nextdenovo.xml Thu Feb 09 21:24:58 2023 +0000 @@ -0,0 +1,220 @@ +<tool id="nextdenovo" name="NextDenovo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> + <description>string graph-based de novo assembler for long reads</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="biotools"/> + <expand macro="requirements" /> + <version_command>nextDenovo --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + mkdir -p './read_files' && + #for $index,$sample in enumerate($input_reads) + #set $ext = $sample.ext + ln -s '${sample}' './read_files/sample_${index}.${ext}' && + #end for + ls './read_files' -1 | sed -e 's|^|read_files/|' > './input.fofn' && + cat '${configfile}' | sed -e "s/cores/\${GALAXY_SLOTS:-4}/g" | sed -e "s|memory|\$((\${GALAXY_MEMORY_MB:-8192}/1024))|g" > './configfile' && + nextDenovo './configfile' + ]]></command> + <configfiles> + <configfile name="configfile"><![CDATA[ + [General] + job_type = local + job_prefix = nextDenovo + task = $task + rewrite = yes + deltmp = yes + parallel_jobs = cores + input_type = $input_type + read_type = $read_type + input_fofn = input.fofn + + [correct_option] + read_cutoff = $read_cutoff + #if $genome_seed.selector == 'genome' + genome_size = $genome_seed.genome_size # estimated genome size + seed_depth = $genome_seed.seed_depth + #else + seed_cutoff = $genome_seed.seed_cutoff + #end if + blocksize = $blocksize + sort_options = -m memoryg -t cores -k $ovl_parameters.max_depth_overlap -l $ovl_parameters.max_over_hang_length + minimap2_options_raw = -t cores --minlen $minimap_parameters.minlen --minmatch $minimap_parameters.minmatch --minide $minimap_parameters.minide --kn $minimap_parameters.kn --wn $minimap_parameters.wn --cn $minimap_parameters.cn --maxhan1 $minimap_parameters.maxhan1 --maxhan2 $minimap_parameters.maxhan2 + pa_correction = cores + correction_options = -p cores + + [assemble_option] + minimap2_options_cns = -t cores + nextgraph_options = -a $np.a $np.c $np.G $np.G $np.k $np.A -E $np.E -q $np.q -i $np.i -I $np.I -R $np.R -S $np.S -r $np.r -M $np.M -T $np.T -N $np.N -u $np.u -w $np.w -D $np.D -P $np.P -m $np.m -n $np.n -B $np.B -C $np.C -z $np.z -l $np.l -L $np.L -t $np.t -F $np.F + ]]></configfile> + </configfiles> + <inputs> + <param name="input_reads" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" multiple="true" label="Sequence reads"/> + <param name="task" type="select" label="Task"> + <option value="all">All</option> + <option value="correct">Correct: only do the correction step</option> + <option value="assemble">Assemble: only do the assembly step (only work if input type = corrected or read type = HiFi)</option> + </param> + <param name="input_type" type="select" label="Input type" help="You can use raw or corrected reads."> + <option value="raw">Raw</option> + <option value="corrected">Corrected</option> + </param> + <param name="read_type" type="select" label="Read type"> + <option value="clr">CLR: continuous long read</option> + <option value="hifi">HiFi: PacBio highly accurate long reads</option> + <option value="ont">ONT: Nanopore 1D reads</option> + </param> + <param name="read_cutoff" type="integer" min="0" value="1000" optional="true" label="Read cutoff" help="filter reads with length smaller than read_cutoff"/> + <conditional name="genome_seed"> + <param name="selector" type="select" label="Provide estimated genome size or seed cutoff" help="It is requried to perform some simple statistics (such as length distribution, total amount of data and sequencing depth) on the input data"> + <option value="genome">Estimated genome size</option> + <option value="seed">Seed cutoff</option> + </param> + <when value="genome"> + <param name="genome_size" type="text" value="" optional="true" label="Estimated genome size" help="Estimated genome size, suffix K/M/G recognized, used to + calculate seed_cutoff/seed_cutfiles/blocksize and average depth, it can be omitted when manually setting seed_cutoff. Spaces are not allowed."> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value="."/> + </valid> + </sanitizer> + <validator type="regex">[0-9KMGkmg.]+</validator> + </param> + <param name="seed_depth" type="integer" min="0" value="45" label="Seed depth" help="Expected seed depth, used to calculate seed_cutoff, co-use with + genome_size, you can try to set it 30-45 to get a better assembly result." /> + </when> + <when value="seed"> + <param name="seed_cutoff" type="integer" min="0" value="0" optional="true" label="Seed cutoff" help="Minimum seed length. Set it to 0 for calculating it automatically." /> + </when> + </conditional> + <param name="blocksize" type="text" value="10g" label="Block size" help="Block size for parallel running, split non-seed reads into small files, the maximum size of + each file is blocksize."> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"/> + </sanitizer> + <validator type="regex">[0-9KMGkmg]+</validator> + </param> + <section name="ovl_parameters" title="OVL sort parameters" expanded="true"> + <param name="max_depth_overlap" type="integer" min="0" value="40" label="Max depth of each overlap" help="This value should be equal or smaller than + the average sequencing depth." /> + <param name="max_over_hang_length" type="integer" min="0" value="300" label="Max over hang length to filter"/> + </section> + <section name="minimap_parameters" title="Minimap2 parameters" expanded="true"> + <param name="minlen" type="integer" min="0" value="500" label="Minimum overlap length"/> + <param name="minmatch" type="integer" min="0" value="100" label="Minimum match length"/> + <param name="minide" type="float" min="0" value="0.05" max="1" label="Minimum identity"/> + <param name="kn" type="integer" min="0" value="17" max="28" label="K-mer size"/> + <param name="wn" type="integer" min="0" value="10" label="Minimizer window size"/> + <param name="cn" type="integer" min="0" value="20" label="Re-align for every n reads"/> + <param name="maxhan1" type="integer" min="0" value="5000" label="Maximum over hang length for re-align"/> + <param name="maxhan2" type="integer" min="0" value="500" label="Maximum over hang length for filtering contained reads"/> + </section> + <section name="correction_options" title="Correction options" expanded="true"> + <param name="split" type="boolean" truevalue="--split" falsevalue="" checked="false" label="Split" help="Split the corrected seed with un-corrected regions" /> + <param name="fast" type="boolean" truevalue="-fast" falsevalue="" checked="false" label="Fast" help="0.5-1 times faster mode with a little lower accuracy." /> + </section> + <section name="np" title="NextGraph parameters"> + <param argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Disable pre-filter chimeric reads."/> + <param argument="-G" type="boolean" truevalue="-G" falsevalue="" checked="false" label="Retain potential chimeric edges."/> + <param argument="-k" type="boolean" truevalue="-k" falsevalue="" checked="false" label="Delete complex bubble paths."/> + <param argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" label="Output alternative contigs" + help="For highly heterozygous genomes, it will increase assembly size."/> + <param argument="-a" type="select" label="Output format"> + <option value="1">FASTA</option> + <option value="3">GFA</option> + </param> + <param argument="-E" type="integer" min="0" value="1000" label="Minimum contig length"/> + <param argument="-q" type="integer" min="0" value="0" label="Minimum short branch length" help="By default it is disabled (value = 0)." /> + <param argument="-i" type="float" min="0" max="1" value="0.1" label="Minimum identity of alignmnents"/> + <param argument="-I" type="float" min="0" max="1" value="0.7" label="Minimum test-to-best identity ratio"/> + <param argument="-R" type="float" min="0" max="1" value="0" label="Maximum test-to-best identity ratio"/> + <param argument="-S" type="float" min="0" max="1" value="0.4" label="Minimum test-to-best aligned length ratio"/> + <param argument="-r" type="float" min="0" max="1" value="0.5" label="Maximum test-to-best score ratio of a low quality edge"/> + <param argument="-M" type="float" min="0" max="1" value="0.9" label="Minimum test-to-best aligned matches ratio"/> + <param argument="-T" type="float" min="0" max="1" value="0.6" label="Minimum test-to-best depth ratio of an edge"/> + <param argument="-N" type="integer" min="1" max="2" value="2" label="Minimum valid nodes of a read"/> + <param argument="-u" type="integer" min="1" max="2" value="2" label="Minimum contained number to filter"/> + <param argument="-w" type="integer" min="1" value="3" label="Minimum depth of an edge"/> + <param argument="-D" type="integer" min="0" value="2" label="Depth of BFS to identify chimeric nodes"/> + <param argument="-P" type="integer" min="0" value="2" label="Maximum depth multiple of a node for BFS"/> + <param argument="-m" type="float" min="0" value="1.5" label="Minimum depth multiple of a repeat node"/> + <param argument="-n" type="float" min="0" value="2000" label="Maximum depth multiple of a node"/> + <param argument="-B" type="integer" min="0" value="500" label="Maximum length of a bubble"/> + <param argument="-C" type="integer" min="0" value="20" label="Maximum length of a compound path"/> + <param argument="-z" type="integer" min="0" value="8" label="Maximum length of a z branch"/> + <param argument="-l" type="integer" min="0" value="15" label="Maximum length of a short branch"/> + <param argument="-L" type="integer" min="0" value="5" label="Maximal length of a short loop"/> + <param argument="-t" type="integer" min="0" value="500" label="Maximal over hang length of dovetails"/> + <param argument="-F" type="integer" min="0" value="1000" label="Fuzz length for trans-reduction"/> + </section> + </inputs> + <outputs> + <data name="stats" format="txt" from_work_dir="03.ctg_graph/nd.asm.fasta.stat" label="${tool.name} on ${on_string}: stats"> + <filter>task != 'correct'</filter> + </data> + <data name="asmp" format="txt" from_work_dir="03.ctg_graph/nd.asm.p.fasta" label="${tool.name} on ${on_string}: nd.asm.p.fasta"> + <filter>task != 'correct'</filter> + </data> + <data name="asm" format="txt" from_work_dir="03.ctg_graph/nd.asm.fasta.stat" label="${tool.name} on ${on_string}: nd.asm.p.fasta"> + <filter>task != 'correct'</filter> + </data> + <data name="asm" format="txt" from_work_dir="02.cns_align/01.seed_cns.sh.work/seed_cns3" label="${tool.name} on ${on_string}: corrected"> + <filter>task != 'assemble'</filter> + </data> + <data name="config" format="txt" from_work_dir="configfile" label="${tool.name} on ${on_string}: configuration file"/> + </outputs> + <tests> + <!-- Default parameters: correct mode --> + <test expect_num_outputs="2"> + <param name="input_reads" value="nanopore.fasta.gz"/> + <param name="task" value="correct"/> + <param name="input_type" value="raw"/> + <param name="read_type" value="ont"/> + <conditional name="genome_seed"> + <param name="selector" value="genome"/> + <param name="genome_size" value="2k"/> + <param name="seed_depth" value="45"/> + </conditional> + <output name="config"> + <assert_contents> + <has_text text="genome_size = 2k"/> + <has_n_lines n="26"/> + </assert_contents> + </output> + </test> + <test expect_failure="true"> + <param name="input_reads" value="nanopore.fasta.gz"/> + <param name="task" value="all"/> + <param name="input_type" value="raw"/> + <param name="read_type" value="nanopore"/> + <conditional name="genome_seed"> + <param name="selector" value="genome"/> + <param name="genome_size" value="2k"/> + <param name="seed_depth" value="45"/> + </conditional> + <assert_stderr> + <has_text text="The read/seed length is too short, and the assembly result is unexpected and please check the assembly quality carefully." /> + </assert_stderr> + </test> + <test expect_failure="true"> + <param name="input_reads" value="nanopore.fasta.gz"/> + <param name="task" value="assemble"/> + <param name="input_type" value="raw"/> + <param name="read_type" value="nanopore"/> + <conditional name="genome_seed"> + <param name="selector" value="genome"/> + <param name="genome_size" value="2k"/> + <param name="seed_depth" value="45"/> + </conditional> + <assert_stderr> + <has_text text="The read/seed length is too short, and the assembly result is unexpected and please check the assembly quality carefully." /> + </assert_stderr> + </test> + </tests> + <help><![CDATA[ + NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses + a "correct-then-assemble" strategy similar to canu (no correction step for PacBio HiFi reads), but + requires significantly less computing resources and storages. + ]]></help> + <expand macro="citations" /> +</tool> \ No newline at end of file