Mercurial > repos > cstrittmatter > skesa
diff skesa.xml @ 23:e2b708d5c0d3 draft
Fixed default parameters for advanced tab
author | estrain |
---|---|
date | Wed, 17 Oct 2018 22:04:16 -0400 |
parents | 9448df7c25a0 |
children | 280e8868b85e |
line wrap: on
line diff
--- a/skesa.xml Mon Oct 15 17:12:13 2018 -0400 +++ b/skesa.xml Wed Oct 17 22:04:16 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="skesa" name="skesa" version="0.23"> +<tool id="skesa" name="skesa" version="0.24"> <requirements> <requirement type="package" version="2.3.0">skesa</requirement> </requirements> @@ -103,25 +103,25 @@ <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"> + <param name="cores" optional="true" type="integer" label="Number of cores to use (Default=16)" value=""/> + <param name="memory" optional="true" type="integer" label="Memory available (Default=32GB)" value=""/> + <param name="hash_count" optional="true" type="boolean" label="hash counter"/> + <param name="estimated_kmers" optional="true" type="integer" label="Estimated number of unique kmers for bloom filter (Default=100)" value=""/> + <param name="skip" optional="true" type="boolean" label="skip bloom filter, use estimate kmers as the hash"/> + <param name="kmer" optional="true" type="integer" label="Minimal kmer length for assembly (Default=21)" value=""/> + <param name="min_count" optional="true" type="integer" label="Minimal count for kmers retained for comparing alternate choices" value=""/> + <param name="max_kmer_count" optional="true" type="integer" label="Minimum acceptable average count for estimating the maximal kmer length in reads" value=""/> + <param name="vector_percent" optional="true" type="float" label="Count for vectors as a fraction of the read number (0-1,1=disabled)" value=""> <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"> + <param name="insert_size" optional="true" type="integer" label="Expected insert size for paired reads" value=""/> + <param name="steps" optional="true" type="integer" label="Number of assembly iterations from minimal to maximal kmer length in reads (Default=11)" value=""/> + <param name="fraction" optional="true" type="float" label="Maximum noise to signal ratio acceptable for extension (Default=0.1)" value=""> <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"/> + <param name="max_snp_len" optional="true" type="integer" label="Maximal snp length (Default=150)" value=""/> + <param name="min_contig" optional="true" type="integer" label="Minimal contig length reported in output (Default=200)" value=""/> + <param name="allow_snps" optional="true" type="boolean" label="Turn SNP discovery (Default=false)"/> </when> <when value="basic"/> </conditional>