Mercurial > repos > iuc > meryl_count_kmers

comparison count-kmers.xml @ 1:52cfaa8d7b1c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl commit 6935ad9dddbbb913817552d682d0b2208481dc7f
author iuc
date Sun, 09 Nov 2025 18:35:01 +0000
parents e377b0f8efda
children
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0:e377b0f8efda 1:52cfaa8d7b1c
34 <option value="count">Count: count the occurrences of canonical k-mers</option> 34 <option value="count">Count: count the occurrences of canonical k-mers</option>
35 <option value="count-forward">Count-forward: count the occurreces of forward k-mers</option> 35 <option value="count-forward">Count-forward: count the occurreces of forward k-mers</option>
36 <option value="count-reverse">Count-reverse: count the occurreces of reverse k-mers</option> 36 <option value="count-reverse">Count-reverse: count the occurreces of reverse k-mers</option>
37 </param> 37 </param>
38 <param name="input_reads" type="data" format="fastq,fastq.gz,fasta,fasta.gz" label="Input sequences" help="Select your reads in FASTA/FASTQ format."/> 38 <param name="input_reads" type="data" format="fastq,fastq.gz,fasta,fasta.gz" label="Input sequences" help="Select your reads in FASTA/FASTQ format."/>
39 <conditional name="options_kmer_size"> 39 <expand macro="kmer_param"/>
40 <param name="kmer_size" type="select" label="K-mer size selector">
41 <option value="provide">Set a k-mer size</option>
42 <option value="estimate">Estimate the best k-mer size</option>
43 </param>
44 <when value="provide">
45 <param name="input_kmer_size" type="integer" min="1" max="50" value="" label="K-mer size" help="For a human genome, the best k-mer size is k=21 for both haploid (3.1G) or diploid (6.2G).."/>
46 </when>
47 <when value="estimate">
48 <param name="genome_size" type="integer" min="1000" max="70000000000" value="1000" label="Genome size" help="Haploid genome size or diploid genome size, depending on what we evaluate. In bp. Only required if the k-mer size is not provided."/>
49 <param name="collision_rate" type="float" min="0.0001" max="0.01" value="0.001" label="Tolerable collision rate" help="Tolerable collision rate. By default is 0.001."/>
50 </when>
51 </conditional>
52 </inputs> 40 </inputs>
53 <outputs> 41 <outputs>
54 <data name="read_db" format="meryldb" from_work_dir="read-db.meryldb"/> 42 <data name="read_db" format="meryldb" from_work_dir="read-db.meryldb"/>
55 </outputs> 43 </outputs>
56 <tests> 44 <tests>