Mask multiple sequence alignments
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’ ]
unmaskedaln
:file
multiple sequence alignment, Stockholm or other formats
*
fmask_rf
:boolean
Flag to output optional file with final mask of non-gap RF len
fmask_all
Flag to output optional file with final mask of full aln len
gmask_rf
Flag to output optional file gap-based 0/1 mask of non-gap RF len
gmask_all
Flag to output optional file gap-based 0/1 mask of full aln len
pmask_rf
Flag to output optional file with PP-based 0/1 mask of non-gap RF len
pmask_all
Flag to output optional file with PP-based 0/1 mask of full aln len
maskfile
mask file, see program documentation
maskedaln
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
*.masked.sthlm.gz
Masked alignment in gzipped Stockholm format
*.sthlm.gz
*.fmask-rf.gz
File with final mask of non-gap RF len
*.fmask-all.gz
File with final mask of full aln len
*.gmask-rf.gz
File with gap-based 0/1 mask of non-gap RF len
*.gmask-all.gz
File with gap-based 0/1 mask of full aln len
*.pmask-rf.gz
File with PP-based 0/1 mask of non-gap RF len
*.pmask-all.gz
File with PP-based 0/1 mask of full aln len
versions_hmmer
${task.process}
:string
The name of the process
hmmer
The name of the tool
hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//'
:eval
The expression to obtain the version of the tool
versions_easel
easel
esl-alimask -h | sed '2!d;s/^# Easel *//;s/ .*//'
versions
Biosequence analysis using profile hidden Markov models
