Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 25:b9cd7722d51b

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"planemo upload"
author kkonganti
date Wed, 29 Jun 2022 12:45:02 -0400
parents 05b6b4edfd58
children 2fb6c7a719d4
comparison
equal deleted inserted replaced
24:05b6b4edfd58 25:b9cd7722d51b
28 --fq_suffix '${fq_suffix}' 28 --fq_suffix '${fq_suffix}'
29 --fq_filename_delim '${fq_filename_delim}' 29 --fq_filename_delim '${fq_filename_delim}'
30 --fq_filename_delim_idx $fq_filename_delim_idx 30 --fq_filename_delim_idx $fq_filename_delim_idx
31 --centrifuge_extract_bug '${centrifuge_extract_bug}' 31 --centrifuge_extract_bug '${centrifuge_extract_bug}'
32 --flye_genome_size '${genome_size}' 32 --flye_genome_size '${genome_size}'
33 #if ($long_read_platform == "nanopore_corr"):
34 --flye_nano_corr true --flye_nano_raw false
35 #elif ($long_read_platform == "nanopore_hq"):
36 --flye_nano_hq true --flye_nano_raw false
37 #elif ($long_read_platform == "pacbio_raw"):
38 --flye_pacbio_raw true --flye_nano_raw false
39 #elif ($long_read_platform == "pacbio_corr"):
40 --flye_pacbio_corr true --flye_nano_raw false
41 #elif ($long_read_platform == "pacbio_hifi"):
42 --flye_pacbio_hifi true --flye_nano_raw false
43 #end if
33 -profile $runtime_profile 44 -profile $runtime_profile
34 -resume; 45 -resume;
35 mv './cpipes-output/${pipeline}-multiqc/multiqc_report.html' './multiqc_report.html'; 46 mv './cpipes-output/${pipeline}-multiqc/multiqc_report.html' './multiqc_report.html';
36 mv './cpipes-output/${pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs; 47 mv './cpipes-output/${pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs;
37 ]]></command> 48 ]]></command>
44 </param> 55 </param>
45 <param name="read_lib_layout" type="select" label="Short Read Library Layout" value="single" 56 <param name="read_lib_layout" type="select" label="Short Read Library Layout" value="single"
46 help="If the pipeline is centriflaken_hy (i.e for short reads), what is the library layout? Default: Single-End"> 57 help="If the pipeline is centriflaken_hy (i.e for short reads), what is the library layout? Default: Single-End">
47 <option value="single">Single-End</option> 58 <option value="single">Single-End</option>
48 <option value="paired">Paired-End</option> 59 <option value="paired">Paired-End</option>
60 </param>
61 <param name="long_read_platform" type="select" label="Mention long read sequencing platform and type" value="nanopore_raw"
62 help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS.">
63 <option value="nanopore_raw">Nanopore raw reads, pre-Guppy5 (&lt;20% error)</option>
64 <option value="nanopore_corr">Nanopore reads that were corrected with other methods (&lt;3% error)</option>
65 <option value="nanopore_hq">Nanopore high-quality reads, Guppy5+ SUP or Q20 (5% error)</option>
66 <option value="pacbio_raw">PacBio regular CLR reads (&lt;20% error)</option>
67 <option value="pacbio_corr">PacBio reads that were corrected with other methods (&lt;3% error)</option>
68 <option value="pacbio_hifi">PacBio HiFi reads (&lt;1% error)</option>
49 </param> 69 </param>
50 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/> 70 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/>
51 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ R2"/> 71 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ R2"/>
52 <param name="fq_filename_delim" type="text" value="_" label="File name delimitor by which samples are grouped together (--fq_filename_delim)" 72 <param name="fq_filename_delim" type="text" value="_" label="File name delimitor by which samples are grouped together (--fq_filename_delim)"
53 help="This is the delimitor by which samples are grouped together to display in the final MultiQC report. For example, if your input data sets are mango_replicate1.fastq.gz, mango_replicate2.fastq.gz, orange_replicate1_maryland.fastq.gz, orange_replicate2_maryland.fastq.gz, then to create 2 samples mango and orange, the value for --fq_filename_delim would be _ (underscore) and the value for --fq_filename_delim_idx would be 1, since you want to group by the first word (i.e. mango or orange) after splitting the filename based on _ (underscore)"/> 73 help="This is the delimitor by which samples are grouped together to display in the final MultiQC report. For example, if your input data sets are mango_replicate1.fastq.gz, mango_replicate2.fastq.gz, orange_replicate1_maryland.fastq.gz, orange_replicate2_maryland.fastq.gz, then to create 2 samples mango and orange, the value for --fq_filename_delim would be _ (underscore) and the value for --fq_filename_delim_idx would be 1, since you want to group by the first word (i.e. mango or orange) after splitting the filename based on _ (underscore)"/>