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comparison skesa.xml @ 6:f9b8095f18fe draft

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Uploaded
author estrain
date Thu, 16 Aug 2018 13:38:26 -0400
parents b82a1b3c5b61
children 15d00ca53144
comparison
equal deleted inserted replaced
5:b82a1b3c5b61 6:f9b8095f18fe
11 --fasta $draft 11 --fasta $draft
12 #else if $jobtype.select == "se" 12 #else if $jobtype.select == "se"
13 --fastq $fastq1 13 --fastq $fastq1
14 #else if $jobtype.select == "pe" 14 #else if $jobtype.select == "pe"
15 --fastq $fastq1,$fastq2 --use_paired_ends 15 --fastq $fastq1,$fastq2 --use_paired_ends
16 #else if $jobtype.select == "pe"
17 --fastq $pairedfiles.forward,$pairedfiles.reverse --use_paired_ends
16 #end if 18 #end if
17 #if $cores != 0 19 #if $cores != 0
18 --cores $cores 20 --cores $cores
19 #end if 21 #end if
20 --memory $memory > results.skesa.fasta 22 --memory $memory > results.skesa.fasta
28 </when> 30 </when>
29 <param name="select" type="select" label="Assembly or FASTQ Reads?"> 31 <param name="select" type="select" label="Assembly or FASTQ Reads?">
30 <option value="sra">SRR number</option> 32 <option value="sra">SRR number</option>
31 <option value="asm">Genome Assembly</option> 33 <option value="asm">Genome Assembly</option>
32 <option value="se">Single-End Reads</option> 34 <option value="se">Single-End Reads</option>
33 <option value="pe">Paired-End Reads</option> 35 <option value="pe">Paired-End Reads (Separate Files)</option>
36 <option value="rp">Paired-End Reads (Paired Data Set)</option>
34 <option value="cl">Collection of Reads</option> 37 <option value="cl">Collection of Reads</option>
35 </param> 38 </param>
36 <when value="asm"> 39 <when value="asm">
37 <param name="draft" type="data" format="fasta" label="FASTA" /> 40 <param name="draft" type="data" format="fasta" label="FASTA" />
38 </when> 41 </when>
43 <param name="fastq1" type="data" format="fastq" label="FASTQ" /> 46 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
44 <param name="fastq2" type="data" format="fastq" label="FASTQ" /> 47 <param name="fastq2" type="data" format="fastq" label="FASTQ" />
45 </when> 48 </when>
46 <when value="cl"> 49 <when value="cl">
47 <param type="data_collection" name="collection_files" format="fastq" collection_type="list" label="FASTQS: Must be a Data Set list built from multiple fastq files" /> 50 <param type="data_collection" name="collection_files" format="fastq" collection_type="list" label="FASTQS: Must be a Data Set list built from multiple fastq files" />
51 </when>
52 <when value="rp">
53 <param type="data_collection" name="pairedfiles" format="fastq" collection_type="paired" label="FASTQS: Must be a paired set of forward and reverse fastq files" />
48 </when> 54 </when>
49 </conditional> 55 </conditional>
50 <param name="memory" type="integer" label="Memory available (GB) [integer]" value="16" /> 56 <param name="memory" type="integer" label="Memory available (GB) [integer]" value="16" />
51 <param name="cores" type="integer" label="Number of cores to use (default all) [integer]" value="0" /> 57 <param name="cores" type="integer" label="Number of cores to use (default all) [integer]" value="0" />
52 <param name="kmer" type="integer" label="Minimal kmer length for assembly [default 21] if non are specified " value="0" /> 58 <param name="kmer" type="integer" label="Minimal kmer length for assembly [default 21] if non are specified " value="0" />