From 6bdadf0d29ae3c077eaf823cbabbc5e6e4842e23 Mon Sep 17 00:00:00 2001 From: "Falk Hildebrand (QIB)" Date: Tue, 18 May 2021 15:32:21 +0100 Subject: [PATCH] 205 --- lotus2.pl => lotus2 | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) rename lotus2.pl => lotus2 (99%) diff --git a/lotus2.pl b/lotus2 similarity index 99% rename from lotus2.pl rename to lotus2 index 155c7c3..c2fadf3 100644 --- a/lotus2.pl +++ b/lotus2 @@ -82,7 +82,7 @@ sub systemW; #versioning -my $selfID = "LotuS 2.04"; #release candidate: 2.0 +my $selfID = "LotuS 2.05"; #release candidate: 2.0 #keep track of time my $start = time; @@ -3028,8 +3028,8 @@ sub help { # HELP BLOCK LOTUS2 #HELPPARSEBEGIN -my $usage_string = "perl lotus2.pl -i -o -m/-map "; -my $usage_example = "perl lotus2.pl -i testDir/ -o testOut/ -m testDir/mymap.txt -CL dada2"; +my $usage_string = "lotus2 -i -o -m/-map "; +my $usage_example = "lotus2 -i testDir/ -o testOut/ -m testDir/mymap.txt -CL dada2"; my $basic_heading = "Basic Options"; my %basic_options = ( '-i ', 'In case that fastqFile or fnaFile and qualFile were specified in the mapping file, this has to be the directory with input files', @@ -3054,7 +3054,7 @@ sub help { '-reversePrimer ','give the reverse primer used to amplify DNA region (e.g. 16S primer rev)', '-verbosity <0-3>', 'Level of verbosity from printing all program calls and program output (3) to not even printing errors (0). Default: 1', '-saveDemultiplex <0|1|2|3>', '(1) Saves all demultiplexed reads (unfiltered) in the [outputdir]/demultiplexed folder, for easier data upload. (2) Only saves quality filtered demultiplexed reads and continues LotuS2 run subsequently. (3) Saves demultiplexed file into a single fq, saving sample ID in fastq/a header. (0) No demultiplexed reads are saved. (Default: 0)', - '-taxOnly ', 'Skip most of the lotus pipeline and only run a taxonomic classification on a fasta file. E.g. ./lotus2.pl -taxOnly -refDB SLV', + '-taxOnly ', 'Skip most of the lotus pipeline and only run a taxonomic classification on a fasta file. E.g. lotus2 -taxOnly -refDB SLV', '-redoTaxOnly <0|1>', '(1) Only redo the taxonomic assignments (useful for replacing a DB used on a finished lotus run). (0) Normal lotus run. (Default: 0)', '-keepOfftargets <0|1>', '(0)?!?: keep offtarget hits against offtargetDB in output fasta and otu matrix, default 0', '-keepTmpFiles <0|1>', '(1) save extra tmp files like chimeric OTUs or the raw blast output in extra dir. (0) do not save these. (Default: 0)', @@ -3101,7 +3101,7 @@ sub help { my %other_options = ( '-v', 'Print LotuS2 version', '-check_map ', 'Mapping_file: only checks mapping file and exists.', - '-create_map ', 'mapping_file: creates a new mapping file at location, based on already demultiplexed input (-i) dir. E.g. ./lotus2.pl -create_map mymap.txt -i /home/dir_with_demultiplex_fastq', + '-create_map ', 'mapping_file: creates a new mapping file at location, based on already demultiplexed input (-i) dir. E.g. lotus2 -create_map mymap.txt -i /home/dir_with_demultiplex_fastq', '-link_usearch ', 'Provide the absolute path to your local usearch binary file, this will be installed to be useable with LotuS2 in the future.', ); #HELPPARSEEND @@ -5539,7 +5539,7 @@ sub autoMap{ print "Map is $ofile\n"; print "Please check that all files required are present in map $ofile.\n"; - print "==========================\nTo start analysis:\n./lotus2.pl -m $ofile -i $pathPre/ -o [outdir] [further parameters if desired]\n==========================\n"; + print "==========================\nTo start analysis:\nlotus2 -m $ofile -i $pathPre/ -o [outdir] [further parameters if desired]\n==========================\n"; exit(0); }