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update, test still fails
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@bgruening
bgruening committed Aug 22, 2024
1 parent 346ee85 commit 2aee5f1
Showing 1 changed file with 19 additions and 24 deletions.
43 changes: 19 additions & 24 deletions tools/nextdenovo/nextdenovo.xml
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<import>macros.xml</import>
</macros>
<expand macro="biotools"/>
<expand macro="requirements" />
<expand macro="requirements"/>
<version_command>nextDenovo --version</version_command>
<command detect_errors="exit_code"><![CDATA[
mkdir -p './read_files' &&
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]]></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="input_reads" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" label="Sequence reads" multiple="true"/>
<param name="task" type="select" label="Task">
<option value="all">All</option>
<option value="correct">Correct: only do the correction step</option>
Expand All @@ -71,60 +71,55 @@
<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.">
<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." />
<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." />
<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.">
<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_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="minide" type="float" min="0" max="1" value="0.05" label="Minimum identity"/>
<param name="kn" type="integer" min="0" max="28" value="17" 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." />
<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="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="-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"/>
Expand Down Expand Up @@ -152,10 +147,10 @@
<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 ${on_string}: nd.asm.p.fasta">
<data name="asmp" format="fasta" from_work_dir="03.ctg_graph/nd.asm.p.fasta" label="${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 ${on_string}: nd.asm.p.fasta">
<data name="asm_fasta_stat" format="txt" from_work_dir="03.ctg_graph/nd.asm.fasta.stat" label="${tool.name} on ${on_string}: nd.asm.fasta.stat">
<filter>task != 'correct'</filter>
</data>
<data name="asm" format="txt" from_work_dir="02.cns_align/01.seed_cns.sh.work/seed_cns3" label="${tool.name} on ${on_string}: corrected">
Expand Down Expand Up @@ -193,7 +188,7 @@
<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." />
<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">
Expand All @@ -207,7 +202,7 @@
<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." />
<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>
Expand All @@ -216,5 +211,5 @@
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>
<expand macro="citations"/>
</tool>

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