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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo commit 5890a5b5b51cfe2dc4a1bbe1866ce508a9f9ce9f |
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macros.xml nextdenovo.xml test-data/nanopore.fasta.gz |
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| diff -r 000000000000 -r 733eab97b979 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Feb 09 21:24:58 2023 +0000 |
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| @@ -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> |
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| diff -r 000000000000 -r 733eab97b979 nextdenovo.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nextdenovo.xml Thu Feb 09 21:24:58 2023 +0000 |
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| b'@@ -0,0 +1,220 @@\n+<tool id="nextdenovo" name="NextDenovo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">\n+ <description>string graph-based de novo assembler for long reads</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="biotools"/>\n+ <expand macro="requirements" />\n+ <version_command>nextDenovo --version</version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+ mkdir -p \'./read_files\' &&\n+ #for $index,$sample in enumerate($input_reads)\n+ #set $ext = $sample.ext\n+ ln -s \'${sample}\' \'./read_files/sample_${index}.${ext}\' &&\n+ #end for\n+ ls \'./read_files\' -1 | sed -e \'s|^|read_files/|\' > \'./input.fofn\' &&\n+ cat \'${configfile}\' | sed -e "s/cores/\\${GALAXY_SLOTS:-4}/g" | sed -e "s|memory|\\$((\\${GALAXY_MEMORY_MB:-8192}/1024))|g" > \'./configfile\' &&\n+ nextDenovo \'./configfile\'\n+ ]]></command>\n+ <configfiles>\n+ <configfile name="configfile"><![CDATA[\n+ [General]\n+ job_type = local\n+ job_prefix = nextDenovo\n+ task = $task\n+ rewrite = yes\n+ deltmp = yes\n+ parallel_jobs = cores\n+ input_type = $input_type\n+ read_type = $read_type\n+ input_fofn = input.fofn\n+\n+ [correct_option]\n+ read_cutoff = $read_cutoff\n+ #if $genome_seed.selector == \'genome\'\n+ genome_size = $genome_seed.genome_size # estimated genome size\n+ seed_depth = $genome_seed.seed_depth\n+ #else\n+ seed_cutoff = $genome_seed.seed_cutoff\n+ #end if\n+ blocksize = $blocksize\n+ sort_options = -m memoryg -t cores -k $ovl_parameters.max_depth_overlap -l $ovl_parameters.max_over_hang_length\n+ 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\n+ pa_correction = cores\n+ correction_options = -p cores\n+\n+ [assemble_option]\n+ minimap2_options_cns = -t cores\n+ 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 $np.F\n+ ]]></configfile>\n+ </configfiles>\n+ <inputs>\n+ <param name="input_reads" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz" multiple="true" label="Sequence reads"/>\n+ <param name="task" type="select" label="Task">\n+ <option value="all">All</option>\n+ <option value="correct">Correct: only do the correction step</option>\n+ <option value="assemble">Assemble: only do the assembly step (only work if input type = corrected or read type = HiFi)</option>\n+ </param>\n+ <param name="input_type" type="select" label="Input type" help="You can use raw or corrected reads.">\n+ <option value="raw">Raw</option>\n+ <option value="corrected">Corrected</option>\n+ </param>\n+ <param name="read_type" type="select" label="Read type">\n+ <option value="clr">CLR: continuous long read</option>\n+ <option value="hifi">HiFi: PacBio highly accurate long reads</option>\n+ <option value="ont">ONT: Nanopore 1D reads</option>\n+ </param>\n+ <param name="read_cutoff" type="integer" min="0" value="1000" optional="true" label="Read cutoff" help="filter reads with length smaller than read_cutoff"/>\n+ <conditional name="genome_seed">\n+ <param name="selector" type="select" label="Provide estimated genome size or seed c'..b'min="0" value="5" label="Maximal length of a short loop"/>\n+ <param argument="-t" type="integer" min="0" value="500" label="Maximal over hang length of dovetails"/>\n+ <param argument="-F" type="integer" min="0" value="1000" label="Fuzz length for trans-reduction"/>\n+ </section>\n+ </inputs>\n+ <outputs>\n+ <data name="stats" format="txt" from_work_dir="03.ctg_graph/nd.asm.fasta.stat" label="${tool.name} on ${on_string}: stats">\n+ <filter>task != \'correct\'</filter>\n+ </data>\n+ <data name="asmp" format="txt" from_work_dir="03.ctg_graph/nd.asm.p.fasta" label="${tool.name} on ${on_string}: nd.asm.p.fasta">\n+ <filter>task != \'correct\'</filter>\n+ </data>\n+ <data name="asm" format="txt" from_work_dir="03.ctg_graph/nd.asm.fasta.stat" label="${tool.name} on ${on_string}: nd.asm.p.fasta">\n+ <filter>task != \'correct\'</filter>\n+ </data>\n+ <data name="asm" format="txt" from_work_dir="02.cns_align/01.seed_cns.sh.work/seed_cns3" label="${tool.name} on ${on_string}: corrected">\n+ <filter>task != \'assemble\'</filter>\n+ </data>\n+ <data name="config" format="txt" from_work_dir="configfile" label="${tool.name} on ${on_string}: configuration file"/>\n+ </outputs>\n+ <tests>\n+ <!-- Default parameters: correct mode -->\n+ <test expect_num_outputs="2">\n+ <param name="input_reads" value="nanopore.fasta.gz"/>\n+ <param name="task" value="correct"/>\n+ <param name="input_type" value="raw"/>\n+ <param name="read_type" value="ont"/>\n+ <conditional name="genome_seed">\n+ <param name="selector" value="genome"/>\n+ <param name="genome_size" value="2k"/>\n+ <param name="seed_depth" value="45"/>\n+ </conditional>\n+ <output name="config">\n+ <assert_contents>\n+ <has_text text="genome_size = 2k"/>\n+ <has_n_lines n="26"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_failure="true">\n+ <param name="input_reads" value="nanopore.fasta.gz"/>\n+ <param name="task" value="all"/>\n+ <param name="input_type" value="raw"/>\n+ <param name="read_type" value="nanopore"/>\n+ <conditional name="genome_seed">\n+ <param name="selector" value="genome"/>\n+ <param name="genome_size" value="2k"/>\n+ <param name="seed_depth" value="45"/>\n+ </conditional>\n+ <assert_stderr>\n+ <has_text text="The read/seed length is too short, and the assembly result is unexpected and please check the assembly quality carefully." />\n+ </assert_stderr>\n+ </test>\n+ <test expect_failure="true">\n+ <param name="input_reads" value="nanopore.fasta.gz"/>\n+ <param name="task" value="assemble"/>\n+ <param name="input_type" value="raw"/>\n+ <param name="read_type" value="nanopore"/>\n+ <conditional name="genome_seed">\n+ <param name="selector" value="genome"/>\n+ <param name="genome_size" value="2k"/>\n+ <param name="seed_depth" value="45"/>\n+ </conditional>\n+ <assert_stderr>\n+ <has_text text="The read/seed length is too short, and the assembly result is unexpected and please check the assembly quality carefully." />\n+ </assert_stderr>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+ NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses \n+ a "correct-then-assemble" strategy similar to canu (no correction step for PacBio HiFi reads), but \n+ requires significantly less computing resources and storages.\n+ ]]></help>\n+ <expand macro="citations" />\n+</tool>\n\\ No newline at end of file\n' |
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