Mercurial > repos > cstrittmatter > skesa
diff skesa.xml @ 22:9448df7c25a0 draft
Uploaded
| author | estrain |
|---|---|
| date | Mon, 15 Oct 2018 17:12:13 -0400 |
| parents | 8bafd3d18864 |
| children | e2b708d5c0d3 |
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--- a/skesa.xml Mon Sep 17 06:49:22 2018 -0400 +++ b/skesa.xml Mon Oct 15 17:12:13 2018 -0400 @@ -1,77 +1,136 @@ -<tool id="skesa" name="skesa" version="0.1"> +<tool id="skesa" name="skesa" version="0.23"> <requirements> - <requirement type="package" version="2.2">skesa</requirement> + <requirement type="package" version="2.3.0">skesa</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - - skesa - #if $jobtype.select == "asm" - --fasta $draft - #else if $jobtype.select == "se" - --fastq $fastq - #else if $jobtype.select == "cl" - #set forward=$jobtype.coll.forward - #set reverse=$jobtype.coll.reverse - --fastq $forward,$reverse --use_paired_ends - #else if $jobtype.select == "pe" - --fastq $forward,$reverse --use_paired_ends + + skesa + + #if $jobtype.select == "fasta_single" + #set outname = $jobtype.fasta.name + --fasta $jobtype.fasta + #else if $jobtype.select == "fastq_single" + #set outname = $jobtype.fastq1.name + --fastq $jobtype.fastq1 + #else if $jobtype.select == "fastq_fr" + #set outname = $jobtype.fastq1.name + --fastq $jobtype.fastq1 --fastq $jobtype.fastq2 + #else if $jobtype.select == "fastq_pair" + #set outname = $jobtype.coll.name + --fastq $jobtype.coll.forward --fastq $jobtype.coll.reverse + #end if + #if $options.select=="advanced" + #if $options.cores + --cores $options.cores + #end if + #if $options.memory + --memory $options.memory + #end if + #if $options.hash_count + --hash_count + #end if + #if $options.estimated_kmers + --estimated_kmers $options.estimated.kmers + #end if + #if $options.skip + --skip_bloom_filter + #end if + #if $options.kmer + --kmer $options.kmer + #end if + #if $options.min_count + --min_count $options.min_count + #end if + #if $options.max_kmer_count + --max_kmer_count $options.max_kmer_count + #end if + #if $options.vector_percent + --vector_percent $options.vector_percent + #end if + #if $options.insert_size + --insert_size $options.insert.size + #end if + #if $options.steps + --steps $options.steps + #end if + #if $options.fraction + --fraction $options.fraction + #end if + #if $options.max_snp_len + --max_snp_len $options.max_snp_len + #end if + #if $options.min_contig + --min_contig $options.min_contig + #end if + #if $options.allow_snps + --allow_snps + #end if + #else if $options.select =="basic" + --cores \${GALAXY_SLOTS:-4} + --memory 16 #end if - #if $cores != 0 - --cores $cores - #end if - --memory $memory > results.skesa.fasta - + + > ${outname}.fasta ]]></command> <inputs> <conditional name="jobtype"> - <param name="select" type="select" label="Assembly or FASTQ Reads?"> - <option value="asm">Genome Assembly</option> - <option value="se">Single-End Reads</option> - <option value="pe">Paired-End Reads (Separate Files)</option> - <option value="cl">Paired collection from your history</option> + <param name="select" type="select" label="Select Input"> + <option value="fasta_single">Single FASTA</option> + <option value="fastq_single">Single FASTQ</option> + <option value="fastq_fr">Forward and Reverse FASTQ</option> + <option value="fastq_pair">Paired FASTQ Collection</option> </param> - <when value="asm"> - <param name="draft" type="data" format="fasta" label="FASTA" /> + <when value="fasta_single"> + <param name="fasta" type="data" format="fasta" label="FASTA" /> </when> - <when value="se"> - <param name="fastq" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" /> + <when value="fastq_single"> + <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" /> </when> - <when value="cl"> - <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" /> + <when value="fastq_fr"> + <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Forward FASTQ" /> + <param name="fastq2" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Reverse FASTQ" /> </when> - <when value="pe"> - <param name="forward" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" /> - <param name="reverse" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" /> + <when value="fastq_pair"> + <param name="coll" label="Paired FASTQ" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" /> </when> </conditional> - <param name="memory" type="integer" label="Memory available (GB) [integer]" value="16" /> - <param name="cores" type="integer" label="Number of cores to use (default all) [integer]" value="0" /> - + + <conditional name="options"> + <param name="select" type="select" label="Options Type"> + <option value="basic">Basic</option> + <option value="advanced">Advanced</option> + </param> + <when value="advanced"> + <param name="cores" type="integer" label="Number of cores to use" value="1"/> + <param name="memory" type="integer" label="Memory available (GB, only for sorted counter)" value="16"/> + <param name="hash_count" type="boolean" label="hash counter"/> + <param name="estimated_kmers" type="integer" label="Estimated number of unique kmers for bloom filter" value="100"/> + <param name="skip" type="boolean" label="skip bloom filter, use estimate kmers as the hash"/> + <param name="kmer" type="integer" label="Minimal kmer length for assembly" value="21"/> + <param name="min_count" type="integer" label="Minimal count for kmers retained for comparing alternate choices" value=""/> + <param name="max_kmer_count" type="integer" label="Minimum acceptable average count for estimating the maximal kmer length in reads" value=""/> + <param name="vector_percent" type="float" label="Count for vectors as a fraction of the read number (1=disabled)" value="1"> + <validator type="in_range" message="Must be float(0,1)." min="0" max="1"/> + </param> + <param name="insert_size" type="integer" label="Expected insert size for paired reads (if not provided, it will be estimated)" value=""/> + <param name="steps" type="integer" label="Number of assembly iterations from minimal to maximal kmer length in reads" value="11"/> + <param name="fraction" type="float" label="Maximum noise to signal ratio acceptable for extension" value="0.1"> + <validator type="in_range" message="Must be float(0,1)." min="0" max="1"/> + </param> + <param name="max_snp_len" type="integer" label="Maximal snp length" value="150"/> + <param name="min_contig" type="integer" label="Minimal contig length reported in output" value="200"/> + <param name="allow_snps" type="boolean" label="Turn SNP discovery" value="false"/> + </when> + <when value="basic"/> + </conditional> </inputs> <outputs> - <data format="fasta" label="skesa Results" name="${input.name}.skesa.fasta" from_work_dir="*.fasta"/> + <data format="fasta" name="results.skesa.fasta" label="${tool.name} on ${on_string}: Contigs" from_work_dir="*.fasta"/> </outputs> <help><![CDATA[ - -**Usage: skesa** - -**INPUT** - -A fasta assembly or single or paired end reads test or data set list of fastqs - -**Memory available** - ---memory arg (=32) Memory available (GB) [integer] - - -**Number of cores** - ---cores arg (=0) Number of cores to use (default all) [integer] - -https://github.com/ncbi/ngs-tools/tree/master/tools/skesa/ ]]></help> <citations>