Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 39:36ca1a1156df

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"planemo upload"
author kkonganti
date Thu, 30 Jun 2022 12:34:34 -0400
parents 1d6557e7db72
children 8ea952e3726e
comparison
equal deleted inserted replaced
38:d7c07f2456b4 39:36ca1a1156df
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):
41 --fq_filter_by_len $fq_filter_by_len
42 #end if
40 --fq_filename_delim '${fq_filename_delim}' 43 --fq_filename_delim '${fq_filename_delim}'
41 --fq_filename_delim_idx $fq_filename_delim_idx 44 --fq_filename_delim_idx $fq_filename_delim_idx
42 --centrifuge_extract_bug '${centrifuge_extract_bug}' 45 --centrifuge_extract_bug '${centrifuge_extract_bug}'
43 -profile $runtime_profile 46 -profile $runtime_profile
44 -resume; 47 -resume;
65 <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>
66 <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>
67 <option value="pacbio_hifi">PacBio HiFi reads (&lt;1% error)</option> 70 <option value="pacbio_hifi">PacBio HiFi reads (&lt;1% error)</option>
68 </param> 71 </param>
69 <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"
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)"/>
70 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ R2"/> 75 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ R2"/>
71 <param name="fq_filename_delim" type="text" value="_" label="File name delimitor by which samples are grouped together (--fq_filename_delim)" 76 <param name="fq_filename_delim" type="text" value="_" label="File name delimitor by which samples are grouped together (--fq_filename_delim)"
72 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)"/> 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)"/>
73 <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)" />
74 <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"/>