Mercurial > repos > cstrittmatter > skesa
comparison skesa.xml @ 10:ddb2fec6cf7a draft
Uploaded
| author | estrain |
|---|---|
| date | Thu, 16 Aug 2018 13:58:32 -0400 |
| parents | 9e6af7620b3c |
| children | 1b69d1441486 |
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| 9:9e6af7620b3c | 10:ddb2fec6cf7a |
|---|---|
| 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 == "rp" | 16 #else if $jobtype.select == "rp" |
| 17 --fastq $pairedfiles.forward,$pairedfiles.reverse --use_paired_ends | 17 --fastq $pairedf{'forward'},$pairedf{'reverse'} --use_paired_ends |
| 18 #end if | 18 #end if |
| 19 #if $cores != 0 | 19 #if $cores != 0 |
| 20 --cores $cores | 20 --cores $cores |
| 21 #end if | 21 #end if |
| 22 --memory $memory > results.skesa.fasta | 22 --memory $memory > results.skesa.fasta |
| 48 </when> | 48 </when> |
| 49 <when value="cl"> | 49 <when value="cl"> |
| 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" /> | 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> | 51 </when> |
| 52 <when value="rp"> | 52 <when value="rp"> |
| 53 <param type="data_collection" collection_type="paired" name="pairedfiles" format="fastq" label="FASTQS: Must be a paired set of forward and reverse fastq files" /> | 53 <param type="data_collection" collection_type="paired" name="pairedf" format="fastq" label="FASTQS: Must be a paired set of forward and reverse fastq files" /> |
| 54 </when> | 54 </when> |
| 55 </conditional> | 55 </conditional> |
| 56 <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" /> |
| 57 <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" /> |
| 58 <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" /> |