Fastx command specifications

FASTQ Quality Filter

$ fastq_quality_filter -h
 usage: fastq_quality_filter [-h] [-v] [-q N] [-p N] [-z] [-i INFILE] [-o OUTFILE]

 version 0.0.6
    [-h]         = This helpful help screen.
    [-q N]       = Minimum quality score to keep.
    [-p N]       = Minimum percent of bases that must have [-q] quality.
    [-z]         = Compress output with GZIP.
    [-i INFILE]  = FASTA/Q input file. default is STDIN.
    [-o OUTFILE] = FASTA/Q output file. default is STDOUT.
    [-v]         = Verbose - report number of sequences.
     If [-o] is specified,  report will be printed to STDOUT.
     If [-o] is not specified (and output goes to STDOUT),
     report will be printed to STDERR. 

Cited from Fastx toolkit

FASTX-Toolkit only can output files in compressed format, not use them as input. 

According to the documentation:Some tools can compress the output with GZIP (-z).
Only in one reported case can the input be gzipped:

fasta_clipping_histogram.pl help page includes this: 
INPUT_FILE.FA   = input file (in FASTA format, can be GZIPped)



Cited from https://www.biostars.org/p/83237/