Mercurial > repos > cstrittmatter > skesa
annotate skesa.xml @ 24:280e8868b85e draft default tip
Fixed handling of paired reads
| author | estrain |
|---|---|
| date | Tue, 24 Sep 2019 11:03:40 -0400 |
| parents | e2b708d5c0d3 |
| children |
| rev | line source |
|---|---|
| 23 | 1 <tool id="skesa" name="skesa" version="0.24"> |
| 14 | 2 <requirements> |
| 22 | 3 <requirement type="package" version="2.3.0">skesa</requirement> |
| 14 | 4 </requirements> |
| 5 <command detect_errors="exit_code"><![CDATA[ | |
| 22 | 6 |
| 7 skesa | |
| 8 | |
| 9 #if $jobtype.select == "fasta_single" | |
| 10 #set outname = $jobtype.fasta.name | |
| 11 --fasta $jobtype.fasta | |
| 12 #else if $jobtype.select == "fastq_single" | |
| 13 #set outname = $jobtype.fastq1.name | |
| 14 --fastq $jobtype.fastq1 | |
| 15 #else if $jobtype.select == "fastq_fr" | |
| 16 #set outname = $jobtype.fastq1.name | |
| 24 | 17 --fastq $jobtype.fastq1,$jobtype.fastq2 |
| 22 | 18 #else if $jobtype.select == "fastq_pair" |
| 19 #set outname = $jobtype.coll.name | |
| 24 | 20 --fastq $jobtype.coll.forward,$jobtype.coll.reverse |
| 22 | 21 #end if |
|
21
8bafd3d18864
planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
20
diff
changeset
|
22 |
| 22 | 23 #if $options.select=="advanced" |
| 24 #if $options.cores | |
| 25 --cores $options.cores | |
| 26 #end if | |
| 27 #if $options.memory | |
| 28 --memory $options.memory | |
| 29 #end if | |
| 30 #if $options.hash_count | |
| 31 --hash_count | |
| 32 #end if | |
| 33 #if $options.estimated_kmers | |
| 34 --estimated_kmers $options.estimated.kmers | |
| 35 #end if | |
| 36 #if $options.skip | |
| 37 --skip_bloom_filter | |
| 38 #end if | |
| 39 #if $options.kmer | |
| 40 --kmer $options.kmer | |
| 41 #end if | |
| 42 #if $options.min_count | |
| 43 --min_count $options.min_count | |
| 44 #end if | |
| 45 #if $options.max_kmer_count | |
| 46 --max_kmer_count $options.max_kmer_count | |
| 47 #end if | |
| 48 #if $options.vector_percent | |
| 49 --vector_percent $options.vector_percent | |
| 50 #end if | |
| 51 #if $options.insert_size | |
| 52 --insert_size $options.insert.size | |
| 53 #end if | |
| 54 #if $options.steps | |
| 55 --steps $options.steps | |
| 56 #end if | |
| 57 #if $options.fraction | |
| 58 --fraction $options.fraction | |
| 59 #end if | |
| 60 #if $options.max_snp_len | |
| 61 --max_snp_len $options.max_snp_len | |
| 62 #end if | |
| 63 #if $options.min_contig | |
| 64 --min_contig $options.min_contig | |
| 65 #end if | |
| 66 #if $options.allow_snps | |
| 67 --allow_snps | |
| 68 #end if | |
| 69 #else if $options.select =="basic" | |
| 70 --cores \${GALAXY_SLOTS:-4} | |
| 71 --memory 16 | |
| 14 | 72 #end if |
| 22 | 73 |
| 74 > ${outname}.fasta | |
| 14 | 75 |
| 76 ]]></command> | |
| 77 <inputs> | |
| 78 <conditional name="jobtype"> | |
| 22 | 79 <param name="select" type="select" label="Select Input"> |
| 80 <option value="fasta_single">Single FASTA</option> | |
| 81 <option value="fastq_single">Single FASTQ</option> | |
| 82 <option value="fastq_fr">Forward and Reverse FASTQ</option> | |
| 83 <option value="fastq_pair">Paired FASTQ Collection</option> | |
| 14 | 84 </param> |
| 22 | 85 <when value="fasta_single"> |
| 86 <param name="fasta" type="data" format="fasta" label="FASTA" /> | |
| 14 | 87 </when> |
| 22 | 88 <when value="fastq_single"> |
| 89 <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" /> | |
|
21
8bafd3d18864
planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
cstrittmatter
parents:
20
diff
changeset
|
90 </when> |
| 22 | 91 <when value="fastq_fr"> |
| 92 <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Forward FASTQ" /> | |
| 93 <param name="fastq2" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Reverse FASTQ" /> | |
| 14 | 94 </when> |
| 22 | 95 <when value="fastq_pair"> |
| 96 <param name="coll" label="Paired FASTQ" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" /> | |
| 14 | 97 </when> |
| 98 </conditional> | |
| 22 | 99 |
| 100 <conditional name="options"> | |
| 101 <param name="select" type="select" label="Options Type"> | |
| 102 <option value="basic">Basic</option> | |
| 103 <option value="advanced">Advanced</option> | |
| 104 </param> | |
| 105 <when value="advanced"> | |
| 23 | 106 <param name="cores" optional="true" type="integer" label="Number of cores to use (Default=16)" value=""/> |
| 107 <param name="memory" optional="true" type="integer" label="Memory available (Default=32GB)" value=""/> | |
| 108 <param name="hash_count" optional="true" type="boolean" label="hash counter"/> | |
| 109 <param name="estimated_kmers" optional="true" type="integer" label="Estimated number of unique kmers for bloom filter (Default=100)" value=""/> | |
| 110 <param name="skip" optional="true" type="boolean" label="skip bloom filter, use estimate kmers as the hash"/> | |
| 111 <param name="kmer" optional="true" type="integer" label="Minimal kmer length for assembly (Default=21)" value=""/> | |
| 112 <param name="min_count" optional="true" type="integer" label="Minimal count for kmers retained for comparing alternate choices" value=""/> | |
| 113 <param name="max_kmer_count" optional="true" type="integer" label="Minimum acceptable average count for estimating the maximal kmer length in reads" value=""/> | |
| 114 <param name="vector_percent" optional="true" type="float" label="Count for vectors as a fraction of the read number (0-1,1=disabled)" value=""> | |
| 22 | 115 <validator type="in_range" message="Must be float(0,1)." min="0" max="1"/> |
| 116 </param> | |
| 23 | 117 <param name="insert_size" optional="true" type="integer" label="Expected insert size for paired reads" value=""/> |
| 118 <param name="steps" optional="true" type="integer" label="Number of assembly iterations from minimal to maximal kmer length in reads (Default=11)" value=""/> | |
| 119 <param name="fraction" optional="true" type="float" label="Maximum noise to signal ratio acceptable for extension (Default=0.1)" value=""> | |
| 22 | 120 <validator type="in_range" message="Must be float(0,1)." min="0" max="1"/> |
| 121 </param> | |
| 23 | 122 <param name="max_snp_len" optional="true" type="integer" label="Maximal snp length (Default=150)" value=""/> |
| 123 <param name="min_contig" optional="true" type="integer" label="Minimal contig length reported in output (Default=200)" value=""/> | |
| 124 <param name="allow_snps" optional="true" type="boolean" label="Turn SNP discovery (Default=false)"/> | |
| 22 | 125 </when> |
| 126 <when value="basic"/> | |
| 127 </conditional> | |
| 14 | 128 </inputs> |
| 129 <outputs> | |
| 22 | 130 <data format="fasta" name="results.skesa.fasta" label="${tool.name} on ${on_string}: Contigs" from_work_dir="*.fasta"/> |
| 14 | 131 </outputs> |
| 132 | |
| 133 <help><![CDATA[ | |
| 134 | |
| 135 ]]></help> | |
| 136 <citations> | |
| 137 <citation type="bibtex"> | |
| 138 @misc{pope_dashnow_zobel_holt_raven_schultz_inouye_tomita_2014, | |
| 139 title={skesa: eSKESA is a de-novo sequence read assembler for cultured single isolate genomes | |
| 140 based on DeBruijn graphs. It uses conservative heuristics and is designed to | |
| 141 create breaks at repeat regions in the genome. This leads to excellent sequence | |
| 142 quality but not necessarily a large N50 statistic. It is a multi-threaded | |
| 143 application that scales well with the number of processors. For different runs | |
| 144 with the same inputs, including the order of reads, the order and orientation | |
| 145 of contigs in the output is deterministic. }, | |
| 146 url={https://github.com/ncbi/ngs-tools/tree/master/tools/skesa/}, | |
| 147 author={National Center for Biotechnology Information }, | |
| 148 }</citation> | |
| 149 </citations> | |
| 150 </tool> |