comparison skesa.xml @ 23:e2b708d5c0d3 draft

Fixed default parameters for advanced tab

22:9448df7c25a0

<tool id="skesa" name="skesa" version="0.23">
    <requirements>
      <requirement type="package" version="2.3.0">skesa</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

        <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>

23:e2b708d5c0d3

<tool id="skesa" name="skesa" version="0.24">
    <requirements>
      <requirement type="package" version="2.3.0">skesa</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

        <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" 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" 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" 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>
    </inputs>
    <outputs>