CLI Reference
This page provides documentation for our command line tools.
blast2galaxy
Usage:
blast2galaxy [OPTIONS] COMMAND [ARGS]...
Options:
--version Show the version and exit.
--help Show this message and exit.
Subcommands
blast2galaxy blastn
search nucleotide databases using a nucleotide query
Usage:
blast2galaxy blastn [OPTIONS]
Options:
--profile TEXT ID of the profile as defined in your config
TOML. The profile consists of Galaxy server
credentials and a Galaxy Tool-ID to be used
for your BLAST call [default: default]
--query TEXT Path / filename of file with nucleotide
query sequence(s) [required]
--task [megablast|blastn|blastn-short|dc-megablast]
Task type [default: megablast]
--db TEXT Database name [required]
--evalue TEXT Expectation value cutoff [default: 0.001]
--out TEXT Path / filename of file to store the BLAST
result
--outfmt [0|2|4|5|6|ext|json] Output format [default: 6]
--html Format output as HTML document
--dust [yes|no] Filter out low complexity regions (with
DUST) [default: yes]
--strand [both|plus|minus] Query strand(s) to search against
database/subject [default: both]
--max_hsps INTEGER Maximum number of HSPs (alignments) to keep
for any single query-subject pair
--perc_identity FLOAT RANGE Percent identity cutoff [default: 0.0;
0.0<=x<=100.0]
--word_size INTEGER RANGE Word size for wordfinder algorithm [x>=2]
--ungapped Perform ungapped alignment only?
--parse_deflines Should the query and subject defline(s) be
parsed?
--qcov_hsp_perc FLOAT RANGE Minimum query coverage per hsp (percentage,
0 to 100) [default: 0.0; 0.0<=x<=100.0]
--window_size INTEGER RANGE Multiple hits window size: use 0 to specify
1-hit algorithm, leave blank for default
[x>=1]
--gapopen INTEGER RANGE Cost to open a gap [x>=0]
--gapextend INTEGER RANGE Cost to extend a gap [x>=0]
--help Show this message and exit.
blast2galaxy blastp
search protein databases using a protein query
Usage:
blast2galaxy blastp [OPTIONS]
Options:
--profile TEXT ID of the profile as defined in your config
TOML. The profile consists of Galaxy server
credentials and a Galaxy Tool-ID to be used
for your BLAST call [default: default]
--query TEXT Path / filename of file with nucleotide
query sequence(s) [required]
--task [blastp|blastp-short|blastp-fast]
Task type [default: blastp]
--db TEXT Database name [required]
--evalue TEXT Expectation value cutoff [default: 0.001]
--out TEXT Path / filename of file to store the BLAST
result
--outfmt [0|2|4|5|6|ext|json] Output format [default: 6]
--html Format output as HTML document
--seg [yes|no] Filter out low complexity regions (with SEG)
[default: yes]
--matrix TEXT Scoring matrix name (normally BLOSUM62)
--max_target_seqs INTEGER RANGE
Maximum number of aligned sequences to keep
(value of 5 or more is recommended) Default
= 500 [default: 500; x>=1]
--num_descriptions INTEGER RANGE
Number of database sequences to show one-
line descriptions for. Not applicable for
outfmt > 4. Default = 500 * Incompatible
with: max_target_seqs [default: 500; x>=0]
--num_alignments INTEGER RANGE Number of database sequences to show
alignments for. Default = 250 * Incompatible
with: max_target_seqs [default: 250; x>=0]
--threshold FLOAT RANGE Minimum word score such that the word is
added to the BLAST lookup table [x>=0.0]
--max_hsps INTEGER Maximum number of HSPs (alignments) to keep
for any single query-subject pair
--word_size INTEGER RANGE Word size for wordfinder algorithm [x>=2]
--ungapped Perform ungapped alignment only?
--parse_deflines Should the query and subject defline(s) be
parsed?
--qcov_hsp_perc FLOAT RANGE Minimum query coverage per hsp (percentage,
0 to 100) [default: 0.0; 0.0<=x<=100.0]
--window_size INTEGER RANGE Multiple hits window size: use 0 to specify
1-hit algorithm, leave blank for default
[x>=1]
--gapopen INTEGER RANGE Cost to open a gap [x>=0]
--gapextend INTEGER RANGE Cost to extend a gap [x>=0]
--comp_based_stats TEXT Use composition-based statistics: D or d:
default (equivalent to 2 ); 0 or F or f: No
composition-based statistics; 1:
Composition-based statistics as in NAR
29:2994-3005, 2001; 2 or T or t :
Composition-based score adjustment as in
Bioinformatics 21:902-911, 2005, conditioned
on sequence properties; 3: Composition-based
score adjustment as in Bioinformatics
21:902-911, 2005, unconditionally [default:
2]
--use_sw_tback Compute locally optimal Smith-Waterman
alignments?
--help Show this message and exit.
blast2galaxy blastx
search protein databases using a translated nucleotide query
Usage:
blast2galaxy blastx [OPTIONS]
Options:
--profile TEXT ID of the profile as defined in your config
TOML. The profile consists of Galaxy server
credentials and a Galaxy Tool-ID to be used
for your BLAST call [default: default]
--query TEXT Path / filename of file with nucleotide
query sequence(s) [required]
--task [blastx|blastx-fast] Task type [default: blastx]
--db TEXT Database name [required]
--evalue TEXT Expectation value cutoff [default: 0.001]
--out TEXT Path / filename of file to store the BLAST
result
--outfmt [0|2|4|5|6|ext|json] Output format [default: 6]
--html Format output as HTML document
--seg [yes|no] Filter out low complexity regions (with SEG)
[default: yes]
--matrix TEXT Scoring matrix name (normally BLOSUM62)
--max_target_seqs INTEGER RANGE
Maximum number of aligned sequences to keep
(value of 5 or more is recommended) Default
= 500 [default: 500; x>=1]
--num_descriptions INTEGER RANGE
Number of database sequences to show one-
line descriptions for. Not applicable for
outfmt > 4. Default = 500 * Incompatible
with: max_target_seqs [default: 500; x>=0]
--num_alignments INTEGER RANGE Number of database sequences to show
alignments for. Default = 250 * Incompatible
with: max_target_seqs [default: 250; x>=0]
--threshold FLOAT RANGE Minimum word score such that the word is
added to the BLAST lookup table [x>=0.0]
--max_hsps INTEGER Maximum number of HSPs (alignments) to keep
for any single query-subject pair
--word_size INTEGER RANGE Word size for wordfinder algorithm [x>=2]
--ungapped Perform ungapped alignment only?
--parse_deflines Should the query and subject defline(s) be
parsed?
--qcov_hsp_perc FLOAT RANGE Minimum query coverage per hsp (percentage,
0 to 100) [default: 0.0; 0.0<=x<=100.0]
--window_size INTEGER RANGE Multiple hits window size: use 0 to specify
1-hit algorithm, leave blank for default
[x>=1]
--gapopen INTEGER RANGE Cost to open a gap [x>=0]
--gapextend INTEGER RANGE Cost to extend a gap [x>=0]
--comp_based_stats TEXT Use composition-based statistics: D or d:
default (equivalent to 2 ); 0 or F or f: No
composition-based statistics; 1:
Composition-based statistics as in NAR
29:2994-3005, 2001; 2 or T or t :
Composition-based score adjustment as in
Bioinformatics 21:902-911, 2005, conditioned
on sequence properties; 3: Composition-based
score adjustment as in Bioinformatics
21:902-911, 2005, unconditionally [default:
2]
--help Show this message and exit.
blast2galaxy diamond-blastp
search protein databases using a protein query with DIAMOND
Usage:
blast2galaxy diamond-blastp [OPTIONS]
Options:
--profile TEXT ID of the profile as defined in your config
TOML. The profile consists of Galaxy server
credentials and a Galaxy Tool-ID to be used
for your BLAST call [default: default]
--query TEXT Path / filename of file with nucleotide
query sequence(s) [required]
--task [blastp|blastp-short|blastp-fast]
Task type [default: blastp]
--db TEXT Database name [required]
--evalue TEXT Expectation value cutoff [default: 0.001]
--out TEXT Path / filename of file to store the BLAST
result
--outfmt TEXT Output format [default: 0]
--faster
--fast
--mid-sensitive
--sensitive
--more-sensitive
--very-sensitive
--ultra-sensitive
--strand [both|plus|minus] Query strand(s) to search against
database/subject [default: both]
--matrix TEXT Scoring matrix name (normally BLOSUM62)
[default: BLOSUM62]
--max-target-seqs INTEGER RANGE
Maximum number of aligned sequences to keep
(value of 5 or more is recommended) Default
= 500 [default: 500; x>=1]
--max-hsps INTEGER Maximum number of HSPs (alignments) to keep
for any single query-subject pair
--window INTEGER RANGE Multiple hits window size: use 0 to specify
1-hit algorithm, leave blank for default
[x>=1]
--gapopen INTEGER RANGE Cost to open a gap [x>=0]
--gapextend INTEGER RANGE Cost to extend a gap [x>=0]
--comp-based-stats TEXT Use composition-based statistics: D or d:
default (equivalent to 2 ); 0 or F or f: No
composition-based statistics; 1:
Composition-based statistics as in NAR
29:2994-3005, 2001; 2 or T or t :
Composition-based score adjustment as in
Bioinformatics 21:902-911, 2005, conditioned
on sequence properties; 3: Composition-based
score adjustment as in Bioinformatics
21:902-911, 2005, unconditionally [default:
1]
--help Show this message and exit.
blast2galaxy diamond-blastx
search protein databases using a translated nucleotide query with DIAMOND
Usage:
blast2galaxy diamond-blastx [OPTIONS]
Options:
--profile TEXT ID of the profile as defined in your config
TOML. The profile consists of Galaxy server
credentials and a Galaxy Tool-ID to be used
for your BLAST call [default: default]
--query TEXT Path / filename of file with nucleotide
query sequence(s) [required]
--task [blastp|blastp-short|blastp-fast]
Task type [default: blastp]
--db TEXT Database name [required]
--evalue TEXT Expectation value cutoff [default: 0.001]
--out TEXT Path / filename of file to store the BLAST
result
--outfmt TEXT Output format [default: 0]
--faster
--fast
--mid-sensitive
--sensitive
--more-sensitive
--very-sensitive
--ultra-sensitive
--strand [both|plus|minus] Query strand(s) to search against
database/subject [default: both]
--matrix TEXT Scoring matrix name (normally BLOSUM62)
[default: BLOSUM62]
--max-target-seqs INTEGER RANGE
Maximum number of aligned sequences to keep
(value of 5 or more is recommended) Default
= 500 [default: 500; x>=1]
--max-hsps INTEGER Maximum number of HSPs (alignments) to keep
for any single query-subject pair
--window INTEGER RANGE Multiple hits window size: use 0 to specify
1-hit algorithm, leave blank for default
[x>=1]
--gapopen INTEGER RANGE Cost to open a gap [x>=0]
--gapextend INTEGER RANGE Cost to extend a gap [x>=0]
--comp-based-stats TEXT Use composition-based statistics: D or d:
default (equivalent to 2 ); 0 or F or f: No
composition-based statistics; 1:
Composition-based statistics as in NAR
29:2994-3005, 2001; 2 or T or t :
Composition-based score adjustment as in
Bioinformatics 21:902-911, 2005, conditioned
on sequence properties; 3: Composition-based
score adjustment as in Bioinformatics
21:902-911, 2005, unconditionally [default:
1]
--help Show this message and exit.
blast2galaxy list-dbs
list available databases of a BLAST+ or DIAMOND tool installed on a Galaxy server
Usage:
blast2galaxy list-dbs [OPTIONS]
Options:
--server TEXT Server-ID as in your config TOML [default: default]
--tool TEXT Tool-ID of a tool available on the Galaxy server [required]
--help Show this message and exit.
blast2galaxy list-tools
list available and compatible BLAST+ and DIAMOND tools installed on a Galaxy server
Usage:
blast2galaxy list-tools [OPTIONS]
Options:
--server TEXT Server-ID as in your config TOML [default:
default]
--type [blastn|tblastn|blastp|blastx|diamond]
Type of BLAST search
--help Show this message and exit.
blast2galaxy show-config
Show information about the currently available configuration loaded from a .blast2galaxy.toml file
Usage:
blast2galaxy show-config [OPTIONS]
Options:
--help Show this message and exit.
blast2galaxy tblastn
search translated nucleotide databases using a protein query
Usage:
blast2galaxy tblastn [OPTIONS]
Options:
--profile TEXT ID of the profile as defined in your config
TOML. The profile consists of Galaxy server
credentials and a Galaxy Tool-ID to be used
for your BLAST call [default: default]
--query TEXT Path / filename of file with nucleotide
query sequence(s) [required]
--task [tblastn|tblastn-fast] Task type [default: tblastn]
--db TEXT Database name [required]
--evalue TEXT Expectation value cutoff [default: 0.001]
--out TEXT Path / filename of file to store the BLAST
result
--outfmt [0|2|4|5|6|ext|json] Output format [default: 6]
--html Format output as HTML document
--seg [yes|no] Filter out low complexity regions (with SEG)
[default: yes]
--db_gencode INTEGER Genetic code to use to translate
database/subjects (see user manual for
details) [default: 1]
--matrix TEXT Scoring matrix name (normally BLOSUM62)
--max_target_seqs INTEGER RANGE
Maximum number of aligned sequences to keep
(value of 5 or more is recommended) Default
= 500 [default: 500; x>=1]
--num_descriptions INTEGER RANGE
Number of database sequences to show one-
line descriptions for. Not applicable for
outfmt > 4. Default = 500 * Incompatible
with: max_target_seqs [default: 500; x>=0]
--num_alignments INTEGER RANGE Number of database sequences to show
alignments for. Default = 250 * Incompatible
with: max_target_seqs [default: 250; x>=0]
--threshold FLOAT RANGE Minimum word score such that the word is
added to the BLAST lookup table [x>=0.0]
--max_hsps INTEGER Maximum number of HSPs (alignments) to keep
for any single query-subject pair
--word_size INTEGER RANGE Word size for wordfinder algorithm [x>=2]
--ungapped Perform ungapped alignment only?
--parse_deflines Should the query and subject defline(s) be
parsed?
--qcov_hsp_perc FLOAT RANGE Minimum query coverage per hsp (percentage,
0 to 100) [default: 0.0; 0.0<=x<=100.0]
--window_size INTEGER RANGE Multiple hits window size: use 0 to specify
1-hit algorithm, leave blank for default
[x>=1]
--gapopen INTEGER RANGE Cost to open a gap [x>=0]
--gapextend INTEGER RANGE Cost to extend a gap [x>=0]
--comp_based_stats TEXT Use composition-based statistics: D or d:
default (equivalent to 2 ); 0 or F or f: No
composition-based statistics; 1:
Composition-based statistics as in NAR
29:2994-3005, 2001; 2 or T or t :
Composition-based score adjustment as in
Bioinformatics 21:902-911, 2005, conditioned
on sequence properties; 3: Composition-based
score adjustment as in Bioinformatics
21:902-911, 2005, unconditionally [default:
2]
--help Show this message and exit.