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comparison cfsan_centriflaken.xml @ 6:1e19594944c5

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"planemo upload"
author kkonganti
date Tue, 28 Jun 2022 10:36:51 -0400
parents 8ab30c459b53
children 872994da252c
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5:8ab30c459b53 6:1e19594944c5
46 <option value="paired">Paired-End</option> 46 <option value="paired">Paired-End</option>
47 </param> 47 </param>
48 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/> 48 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/>
49 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ R2"/> 49 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ R2"/>
50 <param name="fq_filename_delim" type="text" value="_" label="File name delimitor by which samples are grouped together (--fq_filename_delim)" 50 <param name="fq_filename_delim" type="text" value="_" label="File name delimitor by which samples are grouped together (--fq_filename_delim)"
51 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_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)"/> 51 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)"/>
52 <param name="fq_filename_delim_idx" type="integer" value="1" label="File name delimitor index (--fq_filename_delimitor_idx)" /> 52 <param name="fq_filename_delim_idx" type="integer" value="1" label="File name delimitor index (--fq_filename_delim_idx)" />
53 <param name="centrifuge_extract_bug" type="text" value="Escherichia coli" label="Reads belonging to this taxa are extracted and a MAG is generated to allow for serotyping"/> 53 <param name="centrifuge_extract_bug" type="text" value="Escherichia coli" label="Reads belonging to this taxa are extracted and a MAG is generated to allow for serotyping"/>
54 <param name="genome_size" type="text" optional="true" value="5.5m" label="Estimated genome size" help="For example, 5m or 2.6g."> 54 <param name="genome_size" type="text" optional="true" value="5.5m" label="Estimated genome size" help="For example, 5m or 2.6g.">
55 <validator type="regex" message="Genome size must be a float or integer, optionally followed by the a unit prefix (kmg)">^([0-9]*[.])?[0-9]+[kmg]?$</validator> 55 <validator type="regex" message="Genome size must be a float or integer, optionally followed by the a unit prefix (kmg)">^([0-9]*[.])?[0-9]+[kmg]?$</validator>
56 </param> 56 </param>
57 <param name="runtime_profile" type="select" label="Run time profile" value="kondagac"> 57 <param name="runtime_profile" type="select" label="Run time profile" value="kondagac">
86 86
87 .. class:: infomark 87 .. class:: infomark
88 88
89 **Purpose** 89 **Purpose**
90 90
91 Centriflaken suite of automated data analysis pipelines based on Nextflow DSL2 developed at CFSAN, FDA. Thess piepelines allow rapid 91 Centriflaken suite of automated data analysis pipelines are based on Nextflow DSL2 developed at CFSAN, FDA. These piepelines allow rapid
92 and effective construction of metagenomic assembled genomes (MAGs) to enable bacterial source-tracking. It is based on methods described in our 92 and effective construction of metagenomic assembled genomes (MAGs) to enable bacterial source-tracking. It is based on methods described in our
93 previous publication (https://doi.org/10.1371/journal.pone.0245172). 93 previous publication (https://doi.org/10.1371/journal.pone.0245172).
94 ---- 94 ----
95 95
96 .. class:: infomark 96 .. class:: infomark