Output format (aln,msa,fas,etc.), default is clipkit.
*
auxiliary_file{:bash}
:file
Optional tab-delimited auxiliary file specifying which sites to keep or
trim. Used in conjunction with the custom site trimming (cst) mode.
*.tsv
Output
name:type
description
pattern
clipkit{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'sample1' ]
${prefix}.${out_extension}{:bash}
:file
Trimmed multiple sequence alignment file.
*.*
log{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'sample1' ]
${prefix}.${out_extension}.log{:bash}
:file
Log file with per-site trimming statistics from ClipKIT execution.
*.log
metadata{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'sample1' ]
${prefix}.${out_extension}.txt{:bash}
:file
Tab-delimited text file with per-site statistics including site position,
parsimony-informativeness status, and whether the site was kept or trimmed.
*.txt
complementary{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'sample1' ]
${prefix}.${out_extension}.complement{:bash}
:file
File containing the trimmed/removed sites from the alignment, i.e. the
complement of the clipkit output. Optional; only produced when the
complementary input is true (passes -c to clipkit).
*.complement
json{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'sample1' ]
${prefix}.${out_extension}.report.json{:bash}
:file
JSON report file with summary statistics of the trimming run.
Optional; only produced when ClipKIT is run with the appropriate reporting flag.
*.report.json
versions_clipkit{:bash}
${task.process}{:bash}
:string
The name of the process
clipkit{:bash}
:string
The name of the tool
clipkit --version 2>&1 | sed 's/clipkit //'{:bash}
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions{:bash}
${task.process}{:bash}
:string
The name of the process
clipkit{:bash}
:string
The name of the tool
clipkit --version 2>&1 | sed 's/clipkit //'{:bash}
:eval
The expression to obtain the version of the tool
Tools
clipkit
MIT
ClipKIT is a fast and flexible alignment trimming tool that keeps
phylogenetically informative sites and removes those with poor phylogenetic signal.
