Make otu table

The purpose of this tool is to group reads in OTUs and count the number of reads
within each OTU. Most of the time this will be amplicon data (e.g. eDNA metabarcoding)
that has been sequenced on an NGS platform (Illumina, IonTorrent, etc). Before the
"Make otu table" tool can be used reads should at least be merged (assuming
paired-end data) and preferably trimmed.

*.fastq.gz pairs need to be in the format "filename.R1.fastq.gz" and "filename.R2.gz"

"Merge reads" will only accept zip files. Use "Manage ZIP" to zip the fastq.gz pairs.\

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Temporary files created by 'Make otu table' are stored in /media/GalaxyData/database/files/
- these are only visible if "rm -rf $outlocation" in make-otu-table.sh (last line) is turned off
(comment). By default only galaxy has full permissions on these temporary files. This is
inconvenient when trying to access these files as ubuntu (/media is not inside the galaxy home
folder) with sshfs. Change permissions to access these files from the ubuntu-mount:

sudo chmod -R 777 /media/GalaxyData/database/files/

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Sorting of output files otu table (otutab.txt) and sequences(otu_sequences.fa) is done with
the .sh script. Dada2, Usearch and Vsearch commands are invoked by the .py script (the latter
two under "def usearch_cluster(outputFolder)".

if args.cluster == "cluster_otus":
out, error = Popen(["usearch11", "-cluster_otus", outputFolder+"/uniques_sorted.fa", "-uparseout", outputFolder+"/cluster_file.txt", "-otus", outputFolder+"/otu_sequences.fa", "-relabel", "Otu", "-fulldp"], stdout=PIPE, stderr=PIPE).communicate()
admin_log(outputFolder, out=out.decode(), error=error.decode(), function="cluster_otus")

basically means:
usearch11 -cluster_otus followwed by all options/positional arguments (cluster_otus = Uparse).

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Make sure the right file type is selected!
If you provide a fasta file (can only be vsearch which allows both fasta/fastq; dada2 requires fastq)
make sure the file type is not set to fastq (which is the default), otherwise a memmory error will occur: