From a30909883197f0a98fc74bc6ec9655501b7a71b0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20D=C3=ADaz=20Roussel?= Date: Fri, 26 Jan 2024 11:04:10 +0100 Subject: [PATCH] Mark v1.4 and v2 parameters --- docs/source/usage.rst | 176 ++++++++++++++++++++------------------- include/RawText/menu.txt | 74 ++++++++-------- 2 files changed, 129 insertions(+), 121 deletions(-) diff --git a/docs/source/usage.rst b/docs/source/usage.rst index 78367e64c..0ea52001e 100644 --- a/docs/source/usage.rst +++ b/docs/source/usage.rst @@ -1,6 +1,8 @@ Usage *********************** +Here we show all the options that trimAl offers to the user. Some parameters are only available on v2. At the bottom there are some examples of how to use the tool. + Basic usage ================= :: @@ -10,7 +12,7 @@ Basic usage Help Options ================= -.. option:: --help +.. option:: -h Print this information and show some examples. @@ -18,7 +20,7 @@ Help Options Print the trimAl version. -.. option:: -v , --verbose +.. option:: -v , --verbose (v2) Specify the verbose level of the program. Available options: error / 3, warning / 2, info / 1, none / 0 @@ -29,15 +31,19 @@ Input-Output Options .. option:: -in Input file in several formats. - Available input formats: clustal, fasta, mega_interleaved, mega_sequential, nexus, phylip32, phylip40, phylip_paml, pir + Available input formats: clustal, fasta, mega_interleaved (v2), mega_sequential (v2), nexus, phylip32, phylip40, phylip_paml (v2), pir   -.. option:: -formats +.. option:: -formats (v2) Specify one or more formats to save the resulting MSA. Separated by spaces Combinations with specific format arguments (-fasta, -nexus, etc) is allowed. Available output formats: clustal, fasta_m10, fasta, html, mega_sequential, nexus_m10, nexus, phylip32_m10, phylip32, phylip40_m10, phylip40, phylip_paml_m10, phylip_paml, pir -  -.. option:: -out + +.. option:: -out (v1.4) + + Output alignment in the same input format (default stdout). + +.. option:: -out (v2) Output path pattern. (default stdout).   @@ -76,10 +82,68 @@ Input-Output Options trimal -in file1.fasta -out ./[in]/trimmed.[format] -formats fasta -> ./file1/trimmed.fasta (ONLY if folder file1 already exists) -.. option:: -lf, --listformats +.. option:: -lf, --listformats (v2) - List available formats to load from and save to. + List available formats to load from and save to.  + +Legacy Output Options +===================== + +These options are included in v2 for back-compatibility with older versions of trimAl. +New formats will not be added to this list of output format arguments. +The new formats argument "-formats " should be used instead. + +.. option:: -nbrf + + Output file in NBRF/PIR format + +.. option:: -mega + + Output file in MEGA format + +.. option:: -nexus + + Output file in NEXUS format + +.. option:: -clustal + + Output file in CLUSTAL format + +.. option:: -fasta + + Output file in FASTA format + +.. option:: -fasta_m10 + + Output file in FASTA format. + Sequences name length up to 10 characters. + +.. option:: -phylip + + Output file in PHYLIP/PHYLIP4 format. + +.. option:: -phylip_m10 + + Output file in PHYLIP/PHYLIP4 format. + Sequences name length up to 10 characters. + +.. option:: -phylip_paml + + Output file in PHYLIP format compatible with PAML. + +.. option:: -phylip_paml_m10 + + Output file in PHYLIP format compatible with PAML. + Sequences name length up to 10 characters. + +.. option:: -phylip3.2 + + Output file in PHYLIP3.2 format. +.. option:: -phylip3.2_m10 + + Output file in PHYLIP3.2 format. + Sequences name length up to 10 characters. Report Output ==================== @@ -87,11 +151,11 @@ Report Output Get a summary of trimal's work in an HTML file. -.. option:: -svgout +.. option:: -svgout (v2) Get a summary of trimal's work in a SVG file. -.. option:: -sgvstats +.. option:: -sgvstats (v2) Get a summary of trimal's calculated stats in a SVG file. @@ -125,10 +189,14 @@ Backtranslation Options Trimming Parameters ======================= -.. option:: --degenerated_nt_identity +.. option:: --degenerated_nt_identity (v2) Specify the degenerated nt identity matrix as the similarity matrix to use. +.. option:: --alternative_matrix (v1.4) + + Select an alternative similarity matrix already loaded. Only available 'degenerated_nt_identity'. + .. option:: -matrix Input file for user-defined similarity matrix (default is Blosum62). @@ -152,7 +220,8 @@ Trimming Parameters Get the complementary alignment in residues. Reverses the effect of residue trimming: All residues that were to be removed are kept and vice versa. -.. option:: -complementaryseq + +.. option:: -complementaryseq (v2) Get the complementary alignment in sequences. Reverses the effect of sequence trimming: @@ -189,7 +258,7 @@ Manual Trimming - Thresholds Range: [0 - 1] Not compatible with -gat. -.. option:: -gat -gapabsolutethreshold +.. option:: -gat -gapabsolutethreshold (v2) Max number of gaps allowed on a column to keep it. Range: [0 - (number of sequences - 1)] @@ -241,10 +310,6 @@ Overlap Trimming in order to be conserved. Range: [0 - 100](see User Guide). - -Automated ------------- - .. option:: -nogaps Remove all positions with gaps in the alignment. @@ -253,11 +318,14 @@ Automated Remove columns composed only by gaps. -.. option:: -noduplicateseqs +.. option:: -noduplicateseqs (v2) Removes sequences that are equal on the alignment. It will keep the latest sequence in the alignment. +Automated +------------ + .. option:: -gappyout Use automated selection on "gappyout" mode. @@ -351,15 +419,15 @@ Statistics to be calculated and outputted by trimAl Print overlap scores matrix for all sequences in the input alignment. (see User Guide). -NGS Support - VCF SNP MSA creator -==================================== +NGS Support - VCF SNP MSA creator (v2) +====================================== Suport for VCF files. Providing a reference genome, and one or more VCF, multiple MSA are created. One MSA for each contig present on the whole VCF-dataset. Each MSA contains the reference sequence and a sequence for each donor, with their SNP applied.   -.. option:: -vcf +.. option:: -vcf (v2) Specify one or more VCF files to produce MSAs using the input file (-in ) as reference genome. @@ -379,83 +447,23 @@ and a sequence for each donor, with their SNP applied. or it doesn't contain the tag "[contig]", the sequences names will have the name of their contig prepended.   -.. option:: -minquality +.. option:: -minquality (v2) Specify the min quality of a SNP in VCF to apply it. Only valid in combination with -vcf.   -.. option:: -mincoverage +.. option:: -mincoverage (v2) Specify the min coverage of a SNP in VCF to apply it. Only valid in combination with -vcf.   -.. option:: -ignoreFilter +.. option:: -ignoreFilter (v2) Ignore vcf-filtered variants in VCF. Only valid in combination with -vcf. Still applies min-quality and min-coverage when provided. -Legacy Options -=============== - -These options are included for back-compatibility with older versions of trimAl. -New formats will not be added to this list of output format arguments. -The new formats argument "-formats " should be used instead. - -.. option:: -nbrf - - Output file in NBRF/PIR format - -.. option:: -mega - - Output file in MEGA format - -.. option:: -nexus - - Output file in NEXUS format - -.. option:: -clustal - - Output file in CLUSTAL format - -.. option:: -fasta - - Output file in FASTA format - -.. option:: -fasta_m10 - - Output file in FASTA format. - Sequences name length up to 10 characters. - -.. option:: -phylip - - Output file in PHYLIP/PHYLIP4 format. - -.. option:: -phylip_m10 - - Output file in PHYLIP/PHYLIP4 format. - Sequences name length up to 10 characters. - -.. option:: -phylip_paml - - Output file in PHYLIP format compatible with PAML. - -.. option:: -phylip_paml_m10 - - Output file in PHYLIP format compatible with PAML. - Sequences name length up to 10 characters. - -.. option:: -phylip3.2 - - Output file in PHYLIP3.2 format. - -.. option:: -phylip3.2_m10 - - Output file in PHYLIP3.2 format. - Sequences name length up to 10 characters. - - Some Examples ====================== diff --git a/include/RawText/menu.txt b/include/RawText/menu.txt index 19d2f72bb..d1b177ef6 100644 --- a/include/RawText/menu.txt +++ b/include/RawText/menu.txt @@ -22,7 +22,7 @@ trimAl webpage: http://trimal.cgenomics.org For a complete list please see the User Guide or visit http://trimal.cgenomics.org [b][u]Help Options[r] - [b]--help[r] + [b]-h[r] Print this information and show some examples. [b]--version[r] Print the trimAl version. @@ -80,6 +80,40 @@ For a complete list please see the User Guide or visit http://trimal.cgenomics.o [b]-lf / --listformats[r] List available formats to load from and save to. +[b][u]Legacy Output Options[r] +These options are included for back-compatibility with older versions of trimAl. +New formats will not be added to this list of output format arguments. +The new formats argument "-formats " should be used instead. + + [b]-nbrf[r] + Output file in NBRF/PIR format + [b]-mega[r] + Output file in MEGA format + [b]-nexus[r] + Output file in NEXUS format + [b]-clustal[r] + Output file in CLUSTAL format + [b]-fasta[r] + Output file in FASTA format + [b]-fasta_m10[r] + Output file in FASTA format. + Sequences name length up to 10 characters. + [b]-phylip[r] + Output file in PHYLIP/PHYLIP4 format + [b]-phylip_m10[r] + Output file in PHYLIP/PHYLIP4 format. + Sequences name length up to 10 characters. + [b]-phylip_paml[r] + Output file in PHYLIP format compatible with PAML + [b]-phylip_paml_m10[r] + Output file in PHYLIP format compatible with PAML. + Sequences name length up to 10 characters. + [b]-phylip3.2[r] + Output file in PHYLIP3.2 format + [b]-phylip3.2_m10[r] + Output file in PHYLIP3.2 format. + Sequences name length up to 10 characters. + [b][u]Report Output[r] [b]-htmlout [r] Get a summary of trimal's work in an HTML file. @@ -146,8 +180,6 @@ For a complete list please see the User Guide or visit http://trimal.cgenomics.o Selection of sequences to be removed from the alignment. Range: [0 - (Number of Sequences - 1)]. (see User Guide). - [b][u]Automated[r] - [b]-nogaps[r] Remove all positions with gaps in the alignment. [b]-noallgaps[r] @@ -157,6 +189,8 @@ For a complete list please see the User Guide or visit http://trimal.cgenomics.o Removes sequences that are equal on the alignment. It will keep the latest sequence in the alignment. + [b][u]Automated[r] + [b]-gappyout[r] Use automated selection on "gappyout" mode. This method only uses information based on gaps' distribution. @@ -301,38 +335,4 @@ Each MSA contains the reference sequence Only valid in combination with -vcf. Still applies min-quality and min-coverage when provided. -[b][u]Legacy Options[r] -These options are included for back-compatibility with older versions of trimAl. -New formats will not be added to this list of output format arguments. -The new formats argument "-formats " should be used instead. - - [b]-nbrf[r] - Output file in NBRF/PIR format - [b]-mega[r] - Output file in MEGA format - [b]-nexus[r] - Output file in NEXUS format - [b]-clustal[r] - Output file in CLUSTAL format - [b]-fasta[r] - Output file in FASTA format - [b]-fasta_m10[r] - Output file in FASTA format. - Sequences name length up to 10 characters. - [b]-phylip[r] - Output file in PHYLIP/PHYLIP4 format - [b]-phylip_m10[r] - Output file in PHYLIP/PHYLIP4 format. - Sequences name length up to 10 characters. - [b]-phylip_paml[r] - Output file in PHYLIP format compatible with PAML - [b]-phylip_paml_m10[r] - Output file in PHYLIP format compatible with PAML. - Sequences name length up to 10 characters. - [b]-phylip3.2[r] - Output file in PHYLIP3.2 format - [b]-phylip3.2_m10[r] - Output file in PHYLIP3.2 format. - Sequences name length up to 10 characters. - )=====" \ No newline at end of file