Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 40:8ea952e3726e

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"planemo upload"
author kkonganti
date Thu, 30 Jun 2022 12:42:22 -0400
parents 36ca1a1156df
children c4cc8c015560
comparison
equal deleted inserted replaced
39:36ca1a1156df 40:8ea952e3726e
35 #end if 35 #end if
36 #end if 36 #end if
37 --input \${pwd_path}/cpipes-input 37 --input \${pwd_path}/cpipes-input
38 --output \${pwd_path}/cpipes-output 38 --output \${pwd_path}/cpipes-output
39 --fq_suffix '${fq_suffix}' 39 --fq_suffix '${fq_suffix}'
40 #if ($fq_filter_by_len > 0): 40 #if ($fq_filter_by_len != "" and int($fq_filter_by_len) > 0):
41 --fq_filter_by_len $fq_filter_by_len 41 --fq_filter_by_len $fq_filter_by_len
42 #end if 42 #end if
43 --fq_filename_delim '${fq_filename_delim}' 43 --fq_filename_delim '${fq_filename_delim}'
44 --fq_filename_delim_idx $fq_filename_delim_idx 44 --fq_filename_delim_idx $fq_filename_delim_idx
45 --centrifuge_extract_bug '${centrifuge_extract_bug}' 45 --centrifuge_extract_bug '${centrifuge_extract_bug}'
68 <option value="pacbio_raw">PacBio regular CLR reads (&lt;20% error)</option> 68 <option value="pacbio_raw">PacBio regular CLR reads (&lt;20% error)</option>
69 <option value="pacbio_corr">PacBio reads that were corrected with other methods (&lt;3% error)</option> 69 <option value="pacbio_corr">PacBio reads that were corrected with other methods (&lt;3% error)</option>
70 <option value="pacbio_hifi">PacBio HiFi reads (&lt;1% error)</option> 70 <option value="pacbio_hifi">PacBio HiFi reads (&lt;1% error)</option>
71 </param> 71 </param>
72 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/> 72 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/>
73 <param name="fq_filter_by_len" value="" type="integer" label="Enter minimum read length to retain before starting the analysis" 73 <param name="fq_filename_delim" type="text" value="_" label="File name delimitor by which samples are grouped together (--fq_filename_delim)"
74 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)"/>
75 <param name="fq_filter_by_len" optional="true" value="" type="integer" label="Enter minimum read length to retain before starting the analysis"
74 help="Keep this option empty to use default values. Default for centriflaken (long reads) is 4000 bp and for centriflaken_hy (short reads) is 75 bp)"/> 76 help="Keep this option empty to use default values. Default for centriflaken (long reads) is 4000 bp and for centriflaken_hy (short reads) is 75 bp)"/>
75 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ R2"/> 77 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ R2"/>
76 <param name="fq_filename_delim" type="text" value="_" label="File name delimitor by which samples are grouped together (--fq_filename_delim)"
77 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)"/>
78 <param name="fq_filename_delim_idx" type="integer" value="1" label="File name delimitor index (--fq_filename_delim_idx)" /> 78 <param name="fq_filename_delim_idx" type="integer" value="1" label="File name delimitor index (--fq_filename_delim_idx)" />
79 <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"/> 79 <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"/>
80 <param name="genome_size" type="text" optional="true" value="5.5m" label="Estimated genome size" help="For example, 5m or 2.6g."> 80 <param name="genome_size" type="text" optional="true" value="5.5m" label="Estimated genome size" help="For example, 5m or 2.6g.">
81 <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> 81 <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>
82 </param> 82 </param>