Mercurial > repos > devteam > ncbi_blast_plus
changeset 3:643338ac83c0 draft
Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
| author | peterjc |
|---|---|
| date | Thu, 23 Aug 2012 09:00:40 -0400 |
| parents | ab1a8640f817 |
| children | 9d5beacae92b |
| files | blastdb.loc.sample blastdb_p.loc.sample blastxml_to_tabular.py blastxml_to_tabular.xml hide_stderr.py ncbi_blast_plus.txt ncbi_blastn_wrapper.xml ncbi_blastp_wrapper.xml ncbi_blastx_wrapper.xml ncbi_tblastn_wrapper.xml ncbi_tblastx_wrapper.xml tool_dependencies.xml tools/ncbi_blast_plus/blastdb.loc.sample tools/ncbi_blast_plus/blastdb_p.loc.sample tools/ncbi_blast_plus/blastxml_to_tabular.py tools/ncbi_blast_plus/blastxml_to_tabular.xml tools/ncbi_blast_plus/hide_stderr.py tools/ncbi_blast_plus/ncbi_blast_plus.txt tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml tools/ncbi_blast_plus/tool_dependencies.xml |
| diffstat | 24 files changed, 1912 insertions(+), 1912 deletions(-) [+] |
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--- a/blastdb.loc.sample Thu Aug 23 07:32:06 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -#This is a sample file distributed with Galaxy that is used to define a -#list of nucleotide BLAST databases, using three columns tab separated -#(longer whitespace are TAB characters): -# -#<unique_id> <database_caption> <base_name_path> -# -#The captions typically contain spaces and might end with the build date. -#It is important that the actual database name does not have a space in it, -#and that the first tab that appears in the line is right before the path. -# -#So, for example, if your database is nt and the path to your base name -#is /depot/data2/galaxy/blastdb/nt/nt.chunk, then the blastdb.loc entry -#would look like this: -# -#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk -# -#and your /depot/data2/galaxy/blastdb/nt directory would contain all of -#your "base names" (e.g.): -# -#-rw-r--r-- 1 wychung galaxy 23437408 2008-04-09 11:26 nt.chunk.00.nhr -#-rw-r--r-- 1 wychung galaxy 3689920 2008-04-09 11:26 nt.chunk.00.nin -#-rw-r--r-- 1 wychung galaxy 251215198 2008-04-09 11:26 nt.chunk.00.nsq -#...etc... -# -#Your blastdb.loc file should include an entry per line for each "base name" -#you have stored. For example: -# -#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk -#wgs_30_Nov_2009 wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk -#test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test -#...etc... -# -#See also blastdb_p.loc which is for any protein BLAST database. -# -#Note that for backwards compatibility with workflows, the unique ID of -#an entry must be the path that was in the original loc file, because that -#is the value stored in the workflow for that parameter. -#
--- a/blastdb_p.loc.sample Thu Aug 23 07:32:06 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +0,0 @@ -#This is a sample file distributed with Galaxy that is used to define a -#list of protein BLAST databases, using three columns tab separated -#(longer whitespace are TAB characters): -# -#<unique_id> <database_caption> <base_name_path> -# -#The captions typically contain spaces and might end with the build date. -#It is important that the actual database name does not have a space in it, -#and that the first tab that appears in the line is right before the path. -# -#So, for example, if your database is NR and the path to your base name -#is /data/blastdb/nr, then the blastdb_p.loc entry would look like this: -# -#nr NCBI NR (non redundant) /data/blastdb/nr -# -#and your /data/blastdb directory would contain all of the files associated -#with the database, /data/blastdb/nr.*. -# -#Your blastdb_p.loc file should include an entry per line for each "base name" -#you have stored. For example: -# -#nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr -#nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr -#...etc... -# -#See also blastdb.loc which is for any nucleotide BLAST database. -#
--- a/blastxml_to_tabular.py Thu Aug 23 07:32:06 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,254 +0,0 @@ -#!/usr/bin/env python -"""Convert a BLAST XML file to 12 column tabular output - -Takes three command line options, input BLAST XML filename, output tabular -BLAST filename, output format (std for standard 12 columns, or ext for the -extended 24 columns offered in the BLAST+ wrappers). - -The 12 columns output are 'qseqid sseqid pident length mismatch gapopen qstart -qend sstart send evalue bitscore' or 'std' at the BLAST+ command line, which -mean: - -====== ========= ============================================ -Column NCBI name Description ------- --------- -------------------------------------------- - 1 qseqid Query Seq-id (ID of your sequence) - 2 sseqid Subject Seq-id (ID of the database hit) - 3 pident Percentage of identical matches - 4 length Alignment length - 5 mismatch Number of mismatches - 6 gapopen Number of gap openings - 7 qstart Start of alignment in query - 8 qend End of alignment in query - 9 sstart Start of alignment in subject (database hit) - 10 send End of alignment in subject (database hit) - 11 evalue Expectation value (E-value) - 12 bitscore Bit score -====== ========= ============================================ - -The additional columns offered in the Galaxy BLAST+ wrappers are: - -====== ============= =========================================== -Column NCBI name Description ------- ------------- ------------------------------------------- - 13 sallseqid All subject Seq-id(s), separated by a ';' - 14 score Raw score - 15 nident Number of identical matches - 16 positive Number of positive-scoring matches - 17 gaps Total number of gaps - 18 ppos Percentage of positive-scoring matches - 19 qframe Query frame - 20 sframe Subject frame - 21 qseq Aligned part of query sequence - 22 sseq Aligned part of subject sequence - 23 qlen Query sequence length - 24 slen Subject sequence length -====== ============= =========================================== - -Most of these fields are given explicitly in the XML file, others some like -the percentage identity and the number of gap openings must be calculated. - -Be aware that the sequence in the extended tabular output or XML direct from -BLAST+ may or may not use XXXX masking on regions of low complexity. This -can throw the off the calculation of percentage identity and gap openings. -[In fact, both BLAST 2.2.24+ and 2.2.25+ have a subtle bug in this regard, -with these numbers changing depending on whether or not the low complexity -filter is used.] - -This script attempts to produce identical output to what BLAST+ would have done. -However, check this with "diff -b ..." since BLAST+ sometimes includes an extra -space character (probably a bug). -""" -import sys -import re - -if sys.version_info[:2] >= ( 2, 5 ): - import xml.etree.cElementTree as ElementTree -else: - from galaxy import eggs - import pkg_resources; pkg_resources.require( "elementtree" ) - from elementtree import ElementTree - -def stop_err( msg ): - sys.stderr.write("%s\n" % msg) - sys.exit(1) - -#Parse Command Line -try: - in_file, out_file, out_fmt = sys.argv[1:] -except: - stop_err("Expect 3 arguments: input BLAST XML file, output tabular file, out format (std or ext)") - -if out_fmt == "std": - extended = False -elif out_fmt == "x22": - stop_err("Format argument x22 has been replaced with ext (extended 24 columns)") -elif out_fmt == "ext": - extended = True -else: - stop_err("Format argument should be std (12 column) or ext (extended 24 columns)") - - -# get an iterable -try: - context = ElementTree.iterparse(in_file, events=("start", "end")) -except: - stop_err("Invalid data format.") -# turn it into an iterator -context = iter(context) -# get the root element -try: - event, root = context.next() -except: - stop_err( "Invalid data format." ) - - -re_default_query_id = re.compile("^Query_\d+$") -assert re_default_query_id.match("Query_101") -assert not re_default_query_id.match("Query_101a") -assert not re_default_query_id.match("MyQuery_101") -re_default_subject_id = re.compile("^Subject_\d+$") -assert re_default_subject_id.match("Subject_1") -assert not re_default_subject_id.match("Subject_") -assert not re_default_subject_id.match("Subject_12a") -assert not re_default_subject_id.match("TheSubject_1") - - -outfile = open(out_file, 'w') -blast_program = None -for event, elem in context: - if event == "end" and elem.tag == "BlastOutput_program": - blast_program = elem.text - # for every <Iteration> tag - if event == "end" and elem.tag == "Iteration": - #Expecting either this, from BLAST 2.2.25+ using FASTA vs FASTA - # <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID> - # <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> - # <Iteration_query-len>406</Iteration_query-len> - # <Iteration_hits></Iteration_hits> - # - #Or, from BLAST 2.2.24+ run online - # <Iteration_query-ID>Query_1</Iteration_query-ID> - # <Iteration_query-def>Sample</Iteration_query-def> - # <Iteration_query-len>516</Iteration_query-len> - # <Iteration_hits>... - qseqid = elem.findtext("Iteration_query-ID") - if re_default_query_id.match(qseqid): - #Place holder ID, take the first word of the query definition - qseqid = elem.findtext("Iteration_query-def").split(None,1)[0] - qlen = int(elem.findtext("Iteration_query-len")) - - # for every <Hit> within <Iteration> - for hit in elem.findall("Iteration_hits/Hit"): - #Expecting either this, - # <Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id> - # <Hit_def>RecName: Full=Rhodopsin</Hit_def> - # <Hit_accession>P56514</Hit_accession> - #or, - # <Hit_id>Subject_1</Hit_id> - # <Hit_def>gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]</Hit_def> - # <Hit_accession>Subject_1</Hit_accession> - # - #apparently depending on the parse_deflines switch - sseqid = hit.findtext("Hit_id").split(None,1)[0] - hit_def = sseqid + " " + hit.findtext("Hit_def") - if re_default_subject_id.match(sseqid) \ - and sseqid == hit.findtext("Hit_accession"): - #Place holder ID, take the first word of the subject definition - hit_def = hit.findtext("Hit_def") - sseqid = hit_def.split(None,1)[0] - # for every <Hsp> within <Hit> - for hsp in hit.findall("Hit_hsps/Hsp"): - nident = hsp.findtext("Hsp_identity") - length = hsp.findtext("Hsp_align-len") - pident = "%0.2f" % (100*float(nident)/float(length)) - - q_seq = hsp.findtext("Hsp_qseq") - h_seq = hsp.findtext("Hsp_hseq") - m_seq = hsp.findtext("Hsp_midline") - assert len(q_seq) == len(h_seq) == len(m_seq) == int(length) - gapopen = str(len(q_seq.replace('-', ' ').split())-1 + \ - len(h_seq.replace('-', ' ').split())-1) - - mismatch = m_seq.count(' ') + m_seq.count('+') \ - - q_seq.count('-') - h_seq.count('-') - #TODO - Remove this alternative mismatch calculation and test - #once satisifed there are no problems - expected_mismatch = len(q_seq) \ - - sum(1 for q,h in zip(q_seq, h_seq) \ - if q == h or q == "-" or h == "-") - xx = sum(1 for q,h in zip(q_seq, h_seq) if q=="X" and h=="X") - if not (expected_mismatch - q_seq.count("X") <= int(mismatch) <= expected_mismatch + xx): - stop_err("%s vs %s mismatches, expected %i <= %i <= %i" \ - % (qseqid, sseqid, expected_mismatch - q_seq.count("X"), - int(mismatch), expected_mismatch)) - - #TODO - Remove this alternative identity calculation and test - #once satisifed there are no problems - expected_identity = sum(1 for q,h in zip(q_seq, h_seq) if q == h) - if not (expected_identity - xx <= int(nident) <= expected_identity + q_seq.count("X")): - stop_err("%s vs %s identities, expected %i <= %i <= %i" \ - % (qseqid, sseqid, expected_identity, int(nident), - expected_identity + q_seq.count("X"))) - - - evalue = hsp.findtext("Hsp_evalue") - if evalue == "0": - evalue = "0.0" - else: - evalue = "%0.0e" % float(evalue) - - bitscore = float(hsp.findtext("Hsp_bit-score")) - if bitscore < 100: - #Seems to show one decimal place for lower scores - bitscore = "%0.1f" % bitscore - else: - #Note BLAST does not round to nearest int, it truncates - bitscore = "%i" % bitscore - - values = [qseqid, - sseqid, - pident, - length, #hsp.findtext("Hsp_align-len") - str(mismatch), - gapopen, - hsp.findtext("Hsp_query-from"), #qstart, - hsp.findtext("Hsp_query-to"), #qend, - hsp.findtext("Hsp_hit-from"), #sstart, - hsp.findtext("Hsp_hit-to"), #send, - evalue, #hsp.findtext("Hsp_evalue") in scientific notation - bitscore, #hsp.findtext("Hsp_bit-score") rounded - ] - - if extended: - sallseqid = ";".join(name.split(None,1)[0] for name in hit_def.split(">")) - #print hit_def, "-->", sallseqid - positive = hsp.findtext("Hsp_positive") - ppos = "%0.2f" % (100*float(positive)/float(length)) - qframe = hsp.findtext("Hsp_query-frame") - sframe = hsp.findtext("Hsp_hit-frame") - if blast_program == "blastp": - #Probably a bug in BLASTP that they use 0 or 1 depending on format - if qframe == "0": qframe = "1" - if sframe == "0": sframe = "1" - slen = int(hit.findtext("Hit_len")) - values.extend([sallseqid, - hsp.findtext("Hsp_score"), #score, - nident, - positive, - hsp.findtext("Hsp_gaps"), #gaps, - ppos, - qframe, - sframe, - #NOTE - for blastp, XML shows original seq, tabular uses XXX masking - q_seq, - h_seq, - str(qlen), - str(slen), - ]) - #print "\t".join(values) - outfile.write("\t".join(values) + "\n") - # prevents ElementTree from growing large datastructure - root.clear() - elem.clear() -outfile.close()
--- a/blastxml_to_tabular.xml Thu Aug 23 07:32:06 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,127 +0,0 @@ -<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.8"> - <description>Convert BLAST XML output to tabular</description> - <command interpreter="python"> - blastxml_to_tabular.py $blastxml_file $tabular_file $out_format - </command> - <inputs> - <param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/> - <param name="out_format" type="select" label="Output format"> - <option value="std" selected="True">Tabular (standard 12 columns)</option> - <option value="ext">Tabular (extended 24 columns)</option> - </param> - </inputs> - <outputs> - <data name="tabular_file" format="tabular" label="BLAST results as tabular" /> - </outputs> - <requirements> - </requirements> - <tests> - <test> - <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> - <param name="out_format" value="std" /> - <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin.tabluar --> - <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted.tabular" ftype="tabular" /> - </test> - <test> - <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> - <param name="out_format" value="ext" /> - <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin_22c.tabluar --> - <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted_ext.tabular" ftype="tabular" /> - </test> - <test> - <param name="blastxml_file" value="blastp_sample.xml" ftype="blastxml" /> - <param name="out_format" value="std" /> - <!-- Note this has some white space differences from the actual blastp output --> - <output name="tabular_file" file="blastp_sample_converted.tabular" ftype="tabular" /> - </test> - <test> - <param name="blastxml_file" value="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" /> - <param name="out_format" value="std" /> - <!-- Note this has some white space differences from the actual blastx output --> - <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted.tabular" ftype="tabular" /> - </test> - <test> - <param name="blastxml_file" value="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" /> - <param name="out_format" value="ext" /> - <!-- Note this has some white space and XXXX masking differences from the actual blastx output --> - <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted_ext.tabular" ftype="tabular" /> - </test> - <test> - <param name="blastxml_file" value="blastx_sample.xml" ftype="blastxml" /> - <param name="out_format" value="std" /> - <!-- Note this has some white space differences from the actual blastx output --> - <output name="tabular_file" file="blastx_sample_converted.tabular" ftype="tabular" /> - </test> - <test> - <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" /> - <param name="out_format" value="std" /> - <!-- Note this has some white space differences from the actual blastp output --> - <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_std.tabular" ftype="tabular" /> - </test> - <test> - <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" /> - <param name="out_format" value="ext" /> - <!-- Note this has some white space differences from the actual blastp output --> - <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_ext.tabular" ftype="tabular" /> - </test> - </tests> - <help> - -**What it does** - -NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of -formats including tabular and a more detailed XML format. A complex workflow -may need both the XML and the tabular output - but running BLAST twice is -slow and wasteful. - -This tool takes the BLAST XML output and by default converts it into the -standard 12 column tabular equivalent: - -====== ========= ============================================ -Column NCBI name Description ------- --------- -------------------------------------------- - 1 qseqid Query Seq-id (ID of your sequence) - 2 sseqid Subject Seq-id (ID of the database hit) - 3 pident Percentage of identical matches - 4 length Alignment length - 5 mismatch Number of mismatches - 6 gapopen Number of gap openings - 7 qstart Start of alignment in query - 8 qend End of alignment in query - 9 sstart Start of alignment in subject (database hit) - 10 send End of alignment in subject (database hit) - 11 evalue Expectation value (E-value) - 12 bitscore Bit score -====== ========= ============================================ - -The BLAST+ tools can optionally output additional columns of information, -but this takes longer to calculate. Most (but not all) of these columns are -included by selecting the extended tabular output. The extra columns are -included *after* the standard 12 columns. This is so that you can write -workflow filtering steps that accept either the 12 or 22 column tabular -BLAST output. - -====== ============= =========================================== -Column NCBI name Description ------- ------------- ------------------------------------------- - 13 sallseqid All subject Seq-id(s), separated by a ';' - 14 score Raw score - 15 nident Number of identical matches - 16 positive Number of positive-scoring matches - 17 gaps Total number of gaps - 18 ppos Percentage of positive-scoring matches - 19 qframe Query frame - 20 sframe Subject frame - 21 qseq Aligned part of query sequence - 22 sseq Aligned part of subject sequence - 23 qlen Query sequence length - 24 slen Subject sequence length -====== ============= =========================================== - -Beware that the XML file (and thus the conversion) and the tabular output -direct from BLAST+ may differ in the presence of XXXX masking on regions -low complexity (columns 21 and 22), and thus also calculated figures like -the percentage idenity (column 3). - - </help> -</tool>
--- a/hide_stderr.py Thu Aug 23 07:32:06 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,49 +0,0 @@ -#!/usr/bin/env python -"""A simple script to redirect stderr to stdout when the return code is zero. - -See https://bitbucket.org/galaxy/galaxy-central/issue/325/ - -Currently Galaxy ignores the return code from command line tools (even if it -is non-zero which by convention indicates an error) and treats any output on -stderr as an error (even though by convention stderr is used for errors or -warnings). - -This script runs the given command line, capturing all stdout and stderr in -memory, and gets the return code. For a zero return code, any stderr (which -should be warnings only) is added to the stdout. That way Galaxy believes -everything is fine. For a non-zero return code, we output stdout as is, and -any stderr, plus the return code to ensure there is some output on stderr. -That way Galaxy treats this as an error. - -Once issue 325 is fixed, this script will not be needed. -""" -import sys -import subprocess - -#Avoid using shell=True when we call subprocess to ensure if the Python -#script is killed, so too is the BLAST process. -try: - words = [] - for w in sys.argv[1:]: - if " " in w: - words.append('"%s"' % w) - else: - words.append(w) - cmd = " ".join(words) - child = subprocess.Popen(sys.argv[1:], - stdout=subprocess.PIPE, stderr=subprocess.PIPE) -except Exception, err: - sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err)) - sys.exit(1) -#Use .communicate as can get deadlocks with .wait(), -stdout, stderr = child.communicate() -return_code = child.returncode - -if return_code: - sys.stdout.write(stdout) - sys.stderr.write(stderr) - sys.stderr.write("Return error code %i from command:\n" % return_code) - sys.stderr.write("%s\n" % cmd) -else: - sys.stdout.write(stdout) - sys.stdout.write(stderr)
--- a/ncbi_blast_plus.txt Thu Aug 23 07:32:06 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,81 +0,0 @@ -Galaxy wrappers for NCBI BLAST+ suite -===================================== - -These wrappers are copyright 2010-2012 by Peter Cock, The James Hutton Institute -(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. -See the licence text below. - -Currently tested with NCBI BLAST 2.2.26+ (i.e. version 2.2.26 of BLAST+), -and do not work with the NCBI 'legacy' BLAST suite (e.g. blastall). - -Note that these wrappers were originally distributed as part of the main -Galaxy repository, but as of August 2012 moved to the Galaxy Tool Shed. -My thanks to Dannon Baker from the Galaxy development team for this assistance -with this. - - -Manual Installation -=================== - -For those not using Galaxy's automated installation from the Tool Shed, put -the XML and Python files under tools/ncbi_blast_plus and add the XML files -to your tool_conf.xml as normal. - -You must tell Galaxy about any system level BLAST databases using configuration -files blastdb.loc (nucleotide databases like NT) and blastdb_p.loc (protein -databases like NR). - -You will also need to install the 'blast_datatypes' from the Tool Shed. This -defines the BLAST XML file format ('blastxml'). - - -History -======= - -v0.0.11 - Final revision as part of the Galaxy main repository, and the - first release via the Tool Shed -v0.0.12 - Implements genetic code option for translation searches. - - Changes <parallelism> to 1000 sequences at a time (to cope with - very large sets of queries where BLAST+ can become memory hungry) - - Include warning that BLAST+ with subject FASTA gives pairwise - e-values - - -Developers -========== - -This script and related tools are being developed on the following hg branch: -http://bitbucket.org/peterjc/galaxy-central/src/tools - -For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball I use -the following command from the Galaxy tools/ncbi_blast_plus folder: - -$ ./make_ncbi_blast_plus.sh - -This similifies ensuring a consistent set of files is bundled each time, -including all the relevant test files. - - -Licence (MIT/BSD style) -======================= - -Permission to use, copy, modify, and distribute this software and its -documentation with or without modifications and for any purpose and -without fee is hereby granted, provided that any copyright notices -appear in all copies and that both those copyright notices and this -permission notice appear in supporting documentation, and that the -names of the contributors or copyright holders not be used in -advertising or publicity pertaining to distribution of the software -without specific prior permission. - -THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL -WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED -WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE -CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT -OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS -OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE -OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE -OR PERFORMANCE OF THIS SOFTWARE. - -NOTE: This is the licence for the Galaxy Wrapper only. BLAST+ and -associated data files are available and licenced separately.
--- a/ncbi_blastn_wrapper.xml Thu Aug 23 07:32:06 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,211 +0,0 @@ -<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.12"> - <description>Search nucleotide database with nucleotide query sequence(s)</description> - <!-- If job splitting is enabled, break up the query file into parts --> - <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism> - <version_command>blastn -version</version_command> - <command interpreter="python">hide_stderr.py -## The command is a Cheetah template which allows some Python based syntax. -## Lines starting hash hash are comments. Galaxy will turn newlines into spaces -blastn --query "$query" -#if $db_opts.db_opts_selector == "db": - -db "${db_opts.database.fields.path}" -#else: - -subject "$db_opts.subject" -#end if --task $blast_type --evalue $evalue_cutoff --out $output1 -##Set the extended list here so if/when we add things, saved workflows are not affected -#if str($out_format)=="ext": - -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" -#else: - -outfmt $out_format -#end if --num_threads 8 -#if $adv_opts.adv_opts_selector=="advanced": -$adv_opts.filter_query -$adv_opts.strand -## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string -## Note -max_target_seqs overrides -num_descriptions and -num_alignments -#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): --max_target_seqs $adv_opts.max_hits -#end if -#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): --word_size $adv_opts.word_size -#end if -$adv_opts.ungapped -$adv_opts.parse_deflines -## End of advanced options: -#end if - </command> - <inputs> - <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> - <conditional name="db_opts"> - <param name="db_opts_selector" type="select" label="Subject database/sequences"> - <option value="db" selected="True">BLAST Database</option> - <option value="file">FASTA file (pairwise e-values)</option> - </param> - <when value="db"> - <param name="database" type="select" label="Nucleotide BLAST database"> - <options from_file="blastdb.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - <param name="subject" type="hidden" value="" /> - </when> - <when value="file"> - <param name="database" type="hidden" value="" /> - <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> - </when> - </conditional> - <param name="blast_type" type="select" display="radio" label="Type of BLAST"> - <option value="megablast">megablast</option> - <option value="blastn">blastn</option> - <option value="blastn-short">blastn-short</option> - <option value="dc-megablast">dc-megablast</option> - <!-- Using BLAST 2.2.24+ this gives an error: - BLAST engine error: Program type 'vecscreen' not supported - <option value="vecscreen">vecscreen</option> - --> - </param> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> - <param name="out_format" type="select" label="Output format"> - <option value="6" selected="True">Tabular (standard 12 columns)</option> - <option value="ext">Tabular (extended 24 columns)</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> - <option value="0 -html">Pairwise HTML</option> - <option value="2">Query-anchored text</option> - <option value="2 -html">Query-anchored HTML</option> - <option value="4">Flat query-anchored text</option> - <option value="4 -html">Flat query-anchored HTML</option> - <!-- - <option value="-outfmt 11">BLAST archive format (ASN.1)</option> - --> - </param> - <conditional name="adv_opts"> - <param name="adv_opts_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic" /> - <when value="advanced"> - <!-- Could use a select (yes, no, other) where other allows setting 'level window linker' --> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" /> - <param name="strand" type="select" label="Query strand(s) to search against database/subject"> - <option value="-strand both">Both</option> - <option value="-strand plus">Plus (forward)</option> - <option value="-strand minus">Minus (reverse complement)</option> - </param> - <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> - <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> - <validator type="in_range" min="0" /> - </param> - <!-- I'd like word_size to be optional, with minimum 4 for blastn --> - <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4."> - <validator type="in_range" min="0" /> - </param> - <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> - <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/> - </when> - </conditional> - </inputs> - <outputs> - <data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}"> - <change_format> - <when input="out_format" value="0" format="txt"/> - <when input="out_format" value="0 -html" format="html"/> - <when input="out_format" value="2" format="txt"/> - <when input="out_format" value="2 -html" format="html"/> - <when input="out_format" value="4" format="txt"/> - <when input="out_format" value="4 -html" format="html"/> - <when input="out_format" value="5" format="blastxml"/> - </change_format> - </data> - </outputs> - <requirements> - <requirement type="binary">blastn</requirement> - </requirements> - <help> - -.. class:: warningmark - -**Note**. Database searches may take a substantial amount of time. -For large input datasets it is advisable to allow overnight processing. - ------ - -**What it does** - -Search a *nucleotide database* using a *nucleotide query*, -using the NCBI BLAST+ blastn command line tool. -Algorithms include blastn, megablast, and discontiguous megablast. - ------ - -**Output format** - -Because Galaxy focuses on processing tabular data, the default output of this -tool is tabular. The standard BLAST+ tabular output contains 12 columns: - -====== ========= ============================================ -Column NCBI name Description ------- --------- -------------------------------------------- - 1 qseqid Query Seq-id (ID of your sequence) - 2 sseqid Subject Seq-id (ID of the database hit) - 3 pident Percentage of identical matches - 4 length Alignment length - 5 mismatch Number of mismatches - 6 gapopen Number of gap openings - 7 qstart Start of alignment in query - 8 qend End of alignment in query - 9 sstart Start of alignment in subject (database hit) - 10 send End of alignment in subject (database hit) - 11 evalue Expectation value (E-value) - 12 bitscore Bit score -====== ========= ============================================ - -The BLAST+ tools can optionally output additional columns of information, -but this takes longer to calculate. Most (but not all) of these columns are -included by selecting the extended tabular output. The extra columns are -included *after* the standard 12 columns. This is so that you can write -workflow filtering steps that accept either the 12 or 24 column tabular -BLAST output. - -====== ============= =========================================== -Column NCBI name Description ------- ------------- ------------------------------------------- - 13 sallseqid All subject Seq-id(s), separated by a ';' - 14 score Raw score - 15 nident Number of identical matches - 16 positive Number of positive-scoring matches - 17 gaps Total number of gaps - 18 ppos Percentage of positive-scoring matches - 19 qframe Query frame - 20 sframe Subject frame - 21 qseq Aligned part of query sequence - 22 sseq Aligned part of subject sequence - 23 qlen Query sequence length - 24 slen Subject sequence length -====== ============= =========================================== - -The third option is BLAST XML output, which is designed to be parsed by -another program, and is understood by some Galaxy tools. - -You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). -The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. -The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. -The two query anchored outputs show a multiple sequence alignment between the query and all the matches, -and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). - -------- - -**References** - -Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214. - - </help> -</tool>
--- a/ncbi_blastp_wrapper.xml Thu Aug 23 07:32:06 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,278 +0,0 @@ -<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.12"> - <description>Search protein database with protein query sequence(s)</description> - <!-- If job splitting is enabled, break up the query file into parts --> - <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism> - <version_command>blastp -version</version_command> - <command interpreter="python">hide_stderr.py -## The command is a Cheetah template which allows some Python based syntax. -## Lines starting hash hash are comments. Galaxy will turn newlines into spaces -blastp --query "$query" -#if $db_opts.db_opts_selector == "db": - -db "${db_opts.database.fields.path}" -#else: - -subject "$db_opts.subject" -#end if --task $blast_type --evalue $evalue_cutoff --out $output1 -##Set the extended list here so if/when we add things, saved workflows are not affected -#if str($out_format)=="ext": - -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" -#else: - -outfmt $out_format -#end if --num_threads 8 -#if $adv_opts.adv_opts_selector=="advanced": -$adv_opts.filter_query --matrix $adv_opts.matrix -## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string -## Note -max_target_seqs overrides -num_descriptions and -num_alignments -#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): --max_target_seqs $adv_opts.max_hits -#end if -#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): --word_size $adv_opts.word_size -#end if -##Ungapped disabled for now - see comments below -##$adv_opts.ungapped -$adv_opts.parse_deflines -## End of advanced options: -#end if - </command> - <inputs> - <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> - <conditional name="db_opts"> - <param name="db_opts_selector" type="select" label="Subject database/sequences"> - <option value="db" selected="True">BLAST Database</option> - <option value="file">FASTA file (pairwise e-values)</option> - </param> - <when value="db"> - <param name="database" type="select" label="Protein BLAST database"> - <options from_file="blastdb_p.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - <param name="subject" type="hidden" value="" /> - </when> - <when value="file"> - <param name="database" type="hidden" value="" /> - <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> - </when> - </conditional> - <param name="blast_type" type="select" display="radio" label="Type of BLAST"> - <option value="blastp">blastp</option> - <option value="blastp-short">blastp-short</option> - </param> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> - <param name="out_format" type="select" label="Output format"> - <option value="6" selected="True">Tabular (standard 12 columns)</option> - <option value="ext">Tabular (extended 24 columns)</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> - <option value="0 -html">Pairwise HTML</option> - <option value="2">Query-anchored text</option> - <option value="2 -html">Query-anchored HTML</option> - <option value="4">Flat query-anchored text</option> - <option value="4 -html">Flat query-anchored HTML</option> - <!-- - <option value="-outfmt 11">BLAST archive format (ASN.1)</option> - --> - </param> - <conditional name="adv_opts"> - <param name="adv_opts_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic" /> - <when value="advanced"> - <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" /> - <param name="matrix" type="select" label="Scoring matrix"> - <option value="BLOSUM90">BLOSUM90</option> - <option value="BLOSUM80">BLOSUM80</option> - <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> - <option value="BLOSUM50">BLOSUM50</option> - <option value="BLOSUM45">BLOSUM45</option> - <option value="PAM250">PAM250</option> - <option value="PAM70">PAM70</option> - <option value="PAM30">PAM30</option> - </param> - <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> - <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> - <validator type="in_range" min="0" /> - </param> - <!-- I'd like word_size to be optional, with minimum 2 for blastp --> - <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."> - <validator type="in_range" min="0" /> - </param> - <!-- - Can't use '-ungapped' on its own, error back is: - Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search - Tried using '-ungapped -comp_based_stats F' and blastp crashed with 'Attempt to access NULL pointer.' - <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" /> - --> - <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/> - </when> - </conditional> - </inputs> - <outputs> - <data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}"> - <change_format> - <when input="out_format" value="0" format="txt"/> - <when input="out_format" value="0 -html" format="html"/> - <when input="out_format" value="2" format="txt"/> - <when input="out_format" value="2 -html" format="html"/> - <when input="out_format" value="4" format="txt"/> - <when input="out_format" value="4 -html" format="html"/> - <when input="out_format" value="5" format="blastxml"/> - </change_format> - </data> - </outputs> - <requirements> - <requirement type="binary">blastp</requirement> - </requirements> - <tests> - <test> - <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> - <param name="database" value="" /> - <param name="evalue_cutoff" value="1e-8" /> - <param name="blast_type" value="blastp" /> - <param name="out_format" value="5" /> - <param name="adv_opts_selector" value="advanced" /> - <param name="filter_query" value="False" /> - <param name="matrix" value="BLOSUM62" /> - <param name="max_hits" value="0" /> - <param name="word_size" value="0" /> - <param name="parse_deflines" value="True" /> - <output name="output1" file="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> - </test> - <test> - <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> - <param name="database" value="" /> - <param name="evalue_cutoff" value="1e-8" /> - <param name="blast_type" value="blastp" /> - <param name="out_format" value="6" /> - <param name="adv_opts_selector" value="advanced" /> - <param name="filter_query" value="False" /> - <param name="matrix" value="BLOSUM62" /> - <param name="max_hits" value="0" /> - <param name="word_size" value="0" /> - <param name="parse_deflines" value="True" /> - <output name="output1" file="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" /> - </test> - <test> - <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> - <param name="database" value="" /> - <param name="evalue_cutoff" value="1e-8" /> - <param name="blast_type" value="blastp" /> - <param name="out_format" value="ext" /> - <param name="adv_opts_selector" value="advanced" /> - <param name="filter_query" value="False" /> - <param name="matrix" value="BLOSUM62" /> - <param name="max_hits" value="0" /> - <param name="word_size" value="0" /> - <param name="parse_deflines" value="True" /> - <output name="output1" file="blastp_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" /> - </test> - <test> - <param name="query" value="rhodopsin_proteins.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="database" value="" /> - <param name="evalue_cutoff" value="1e-8" /> - <param name="blast_type" value="blastp" /> - <param name="out_format" value="6" /> - <param name="adv_opts_selector" value="basic" /> - <output name="output1" file="blastp_rhodopsin_vs_four_human.tabular" ftype="tabular" /> - </test> - </tests> - <help> - -.. class:: warningmark - -**Note**. Database searches may take a substantial amount of time. -For large input datasets it is advisable to allow overnight processing. - ------ - -**What it does** - -Search a *protein database* using a *protein query*, -using the NCBI BLAST+ blastp command line tool. - ------ - -**Output format** - -Because Galaxy focuses on processing tabular data, the default output of this -tool is tabular. The standard BLAST+ tabular output contains 12 columns: - -====== ========= ============================================ -Column NCBI name Description ------- --------- -------------------------------------------- - 1 qseqid Query Seq-id (ID of your sequence) - 2 sseqid Subject Seq-id (ID of the database hit) - 3 pident Percentage of identical matches - 4 length Alignment length - 5 mismatch Number of mismatches - 6 gapopen Number of gap openings - 7 qstart Start of alignment in query - 8 qend End of alignment in query - 9 sstart Start of alignment in subject (database hit) - 10 send End of alignment in subject (database hit) - 11 evalue Expectation value (E-value) - 12 bitscore Bit score -====== ========= ============================================ - -The BLAST+ tools can optionally output additional columns of information, -but this takes longer to calculate. Most (but not all) of these columns are -included by selecting the extended tabular output. The extra columns are -included *after* the standard 12 columns. This is so that you can write -workflow filtering steps that accept either the 12 or 24 column tabular -BLAST output. - -====== ============= =========================================== -Column NCBI name Description ------- ------------- ------------------------------------------- - 13 sallseqid All subject Seq-id(s), separated by a ';' - 14 score Raw score - 15 nident Number of identical matches - 16 positive Number of positive-scoring matches - 17 gaps Total number of gaps - 18 ppos Percentage of positive-scoring matches - 19 qframe Query frame - 20 sframe Subject frame - 21 qseq Aligned part of query sequence - 22 sseq Aligned part of subject sequence - 23 qlen Query sequence length - 24 slen Subject sequence length -====== ============= =========================================== - -The third option is BLAST XML output, which is designed to be parsed by -another program, and is understood by some Galaxy tools. - -You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). -The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. -The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. -The two query anchored outputs show a multiple sequence alignment between the query and all the matches, -and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). - -------- - -**References** - -Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. - -Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005. - - </help> -</tool>
--- a/ncbi_blastx_wrapper.xml Thu Aug 23 07:32:06 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,264 +0,0 @@ -<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.12"> - <description>Search protein database with translated nucleotide query sequence(s)</description> - <!-- If job splitting is enabled, break up the query file into parts --> - <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism> - <version_command>blastx -version</version_command> - <command interpreter="python">hide_stderr.py -## The command is a Cheetah template which allows some Python based syntax. -## Lines starting hash hash are comments. Galaxy will turn newlines into spaces -blastx --query "$query" -#if $db_opts.db_opts_selector == "db": - -db "${db_opts.database.fields.path}" -#else: - -subject "$db_opts.subject" -#end if --query_gencode $query_gencode --evalue $evalue_cutoff --out $output1 -##Set the extended list here so if/when we add things, saved workflows are not affected -#if str($out_format)=="ext": - -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" -#else: - -outfmt $out_format -#end if --num_threads 8 -#if $adv_opts.adv_opts_selector=="advanced": -$adv_opts.filter_query -$adv_opts.strand --matrix $adv_opts.matrix -## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string -## Note -max_target_seqs overrides -num_descriptions and -num_alignments -#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): --max_target_seqs $adv_opts.max_hits -#end if -#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): --word_size $adv_opts.word_size -#end if -$adv_opts.ungapped -$adv_opts.parse_deflines -## End of advanced options: -#end if - </command> - <inputs> - <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> - <conditional name="db_opts"> - <param name="db_opts_selector" type="select" label="Subject database/sequences"> - <option value="db" selected="True">BLAST Database</option> - <option value="file">FASTA file (pairwise e-values)</option> - </param> - <when value="db"> - <param name="database" type="select" label="Protein BLAST database"> - <options from_file="blastdb_p.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - <param name="subject" type="hidden" value="" /> - </when> - <when value="file"> - <param name="database" type="hidden" value="" /> - <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> - </when> - </conditional> - <param name="query_gencode" type="select" label="Query genetic code"> - <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> - <option value="1" select="True">1. Standard</option> - <option value="2">2. Vertebrate Mitochondrial</option> - <option value="3">3. Yeast Mitochondrial</option> - <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> - <option value="5">5. Invertebrate Mitochondrial</option> - <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> - <option value="9">9. Echinoderm Mitochondrial</option> - <option value="10">10. Euplotid Nuclear</option> - <option value="11">11. Bacteria and Archaea</option> - <option value="12">12. Alternative Yeast Nuclear</option> - <option value="13">13. Ascidian Mitochondrial</option> - <option value="14">14. Flatworm Mitochondrial</option> - <option value="15">15. Blepharisma Macronuclear</option> - <option value="16">16. Chlorophycean Mitochondrial Code</option> - <option value="21">21. Trematode Mitochondrial Code</option> - <option value="22">22. Scenedesmus obliquus mitochondrial Code</option> - <option value="23">23. Thraustochytrium Mitochondrial Code</option> - <option value="24">24. Pterobranchia mitochondrial code</option> - </param> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> - <param name="out_format" type="select" label="Output format"> - <option value="6" selected="True">Tabular (standard 12 columns)</option> - <option value="ext">Tabular (extended 24 columns)</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> - <option value="0 -html">Pairwise HTML</option> - <option value="2">Query-anchored text</option> - <option value="2 -html">Query-anchored HTML</option> - <option value="4">Flat query-anchored text</option> - <option value="4 -html">Flat query-anchored HTML</option> - <!-- - <option value="-outfmt 11">BLAST archive format (ASN.1)</option> - --> - </param> - <conditional name="adv_opts"> - <param name="adv_opts_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic" /> - <when value="advanced"> - <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> - <param name="strand" type="select" label="Query strand(s) to search against database/subject"> - <option value="-strand both">Both</option> - <option value="-strand plus">Plus (forward)</option> - <option value="-strand minus">Minus (reverse complement)</option> - </param> - <param name="matrix" type="select" label="Scoring matrix"> - <option value="BLOSUM90">BLOSUM90</option> - <option value="BLOSUM80">BLOSUM80</option> - <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> - <option value="BLOSUM50">BLOSUM50</option> - <option value="BLOSUM45">BLOSUM45</option> - <option value="PAM250">PAM250</option> - <option value="PAM70">PAM70</option> - <option value="PAM30">PAM30</option> - </param> - <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> - <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> - <validator type="in_range" min="0" /> - </param> - <!-- I'd like word_size to be optional, with minimum 2 for blastx --> - <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."> - <validator type="in_range" min="0" /> - </param> - <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> - <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/> - </when> - </conditional> - </inputs> - <outputs> - <data name="output1" format="tabular" label="blastx on ${db_opts.db_opts_selector}"> - <change_format> - <when input="out_format" value="0" format="txt"/> - <when input="out_format" value="0 -html" format="html"/> - <when input="out_format" value="2" format="txt"/> - <when input="out_format" value="2 -html" format="html"/> - <when input="out_format" value="4" format="txt"/> - <when input="out_format" value="4 -html" format="html"/> - <when input="out_format" value="5" format="blastxml"/> - </change_format> - </data> - </outputs> - <requirements> - <requirement type="binary">blastx</requirement> - </requirements> - <tests> - <test> - <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="database" value="" /> - <param name="evalue_cutoff" value="1e-10" /> - <param name="out_format" value="5" /> - <param name="adv_opts_selector" value="basic" /> - <output name="output1" file="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" /> - </test> - <test> - <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="database" value="" /> - <param name="evalue_cutoff" value="1e-10" /> - <param name="out_format" value="6" /> - <param name="adv_opts_selector" value="basic" /> - <output name="output1" file="blastx_rhodopsin_vs_four_human.tabular" ftype="tabular" /> - </test> - <test> - <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="database" value="" /> - <param name="evalue_cutoff" value="1e-10" /> - <param name="out_format" value="ext" /> - <param name="adv_opts_selector" value="basic" /> - <output name="output1" file="blastx_rhodopsin_vs_four_human_ext.tabular" ftype="tabular" /> - </test> - </tests> - <help> - -.. class:: warningmark - -**Note**. Database searches may take a substantial amount of time. -For large input datasets it is advisable to allow overnight processing. - ------ - -**What it does** - -Search a *protein database* using a *translated nucleotide query*, -using the NCBI BLAST+ blastx command line tool. - ------ - -**Output format** - -Because Galaxy focuses on processing tabular data, the default output of this -tool is tabular. The standard BLAST+ tabular output contains 12 columns: - -====== ========= ============================================ -Column NCBI name Description ------- --------- -------------------------------------------- - 1 qseqid Query Seq-id (ID of your sequence) - 2 sseqid Subject Seq-id (ID of the database hit) - 3 pident Percentage of identical matches - 4 length Alignment length - 5 mismatch Number of mismatches - 6 gapopen Number of gap openings - 7 qstart Start of alignment in query - 8 qend End of alignment in query - 9 sstart Start of alignment in subject (database hit) - 10 send End of alignment in subject (database hit) - 11 evalue Expectation value (E-value) - 12 bitscore Bit score -====== ========= ============================================ - -The BLAST+ tools can optionally output additional columns of information, -but this takes longer to calculate. Most (but not all) of these columns are -included by selecting the extended tabular output. The extra columns are -included *after* the standard 12 columns. This is so that you can write -workflow filtering steps that accept either the 12 or 24 column tabular -BLAST output. - -====== ============= =========================================== -Column NCBI name Description ------- ------------- ------------------------------------------- - 13 sallseqid All subject Seq-id(s), separated by a ';' - 14 score Raw score - 15 nident Number of identical matches - 16 positive Number of positive-scoring matches - 17 gaps Total number of gaps - 18 ppos Percentage of positive-scoring matches - 19 qframe Query frame - 20 sframe Subject frame - 21 qseq Aligned part of query sequence - 22 sseq Aligned part of subject sequence - 23 qlen Query sequence length - 24 slen Subject sequence length -====== ============= =========================================== - -The third option is BLAST XML output, which is designed to be parsed by -another program, and is understood by some Galaxy tools. - -You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). -The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. -The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. -The two query anchored outputs show a multiple sequence alignment between the query and all the matches, -and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). - -------- - -**References** - -Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. - - </help> -</tool>
--- a/ncbi_tblastn_wrapper.xml Thu Aug 23 07:32:06 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,310 +0,0 @@ -<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.12"> - <description>Search translated nucleotide database with protein query sequence(s)</description> - <!-- If job splitting is enabled, break up the query file into parts --> - <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism> - <version_command>tblastn -version</version_command> - <command interpreter="python">hide_stderr.py -## The command is a Cheetah template which allows some Python based syntax. -## Lines starting hash hash are comments. Galaxy will turn newlines into spaces -tblastn --query "$query" -#if $db_opts.db_opts_selector == "db": - -db "${db_opts.database.fields.path}" -#else: - -subject "$db_opts.subject" -#end if --evalue $evalue_cutoff --out $output1 -##Set the extended list here so if/when we add things, saved workflows are not affected -#if str($out_format)=="ext": - -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" -#else: - -outfmt $out_format -#end if --num_threads 8 -#if $adv_opts.adv_opts_selector=="advanced": --db_gencode $adv_opts.db_gencode -$adv_opts.filter_query --matrix $adv_opts.matrix -## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string -## Note -max_target_seqs overrides -num_descriptions and -num_alignments -#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): --max_target_seqs $adv_opts.max_hits -#end if -#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): --word_size $adv_opts.word_size -#end if -##Ungapped disabled for now - see comments below -##$adv_opts.ungapped -$adv_opts.parse_deflines -## End of advanced options: -#end if - </command> - <inputs> - <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> - <conditional name="db_opts"> - <param name="db_opts_selector" type="select" label="Subject database/sequences"> - <option value="db" selected="True">BLAST Database</option> - <option value="file">FASTA file (pairwise e-values)</option> - </param> - <when value="db"> - <param name="database" type="select" label="Nucleotide BLAST database"> - <options from_file="blastdb.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - <param name="subject" type="hidden" value="" /> - </when> - <when value="file"> - <param name="database" type="hidden" value="" /> - <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> - </when> - </conditional> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> - <param name="out_format" type="select" label="Output format"> - <option value="6" selected="True">Tabular (standard 12 columns)</option> - <option value="ext">Tabular (extended 24 columns)</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> - <option value="0 -html">Pairwise HTML</option> - <option value="2">Query-anchored text</option> - <option value="2 -html">Query-anchored HTML</option> - <option value="4">Flat query-anchored text</option> - <option value="4 -html">Flat query-anchored HTML</option> - <!-- - <option value="-outfmt 11">BLAST archive format (ASN.1)</option> - --> - </param> - <conditional name="adv_opts"> - <param name="adv_opts_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic" /> - <when value="advanced"> - <param name="db_gencode" type="select" label="Database/subject genetic code"> - <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> - <option value="1" select="True">1. Standard</option> - <option value="2">2. Vertebrate Mitochondrial</option> - <option value="3">3. Yeast Mitochondrial</option> - <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> - <option value="5">5. Invertebrate Mitochondrial</option> - <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> - <option value="9">9. Echinoderm Mitochondrial</option> - <option value="10">10. Euplotid Nuclear</option> - <option value="11">11. Bacteria and Archaea</option> - <option value="12">12. Alternative Yeast Nuclear</option> - <option value="13">13. Ascidian Mitochondrial</option> - <option value="14">14. Flatworm Mitochondrial</option> - <option value="15">15. Blepharisma Macronuclear</option> - <option value="16">16. Chlorophycean Mitochondrial Code</option> - <option value="21">21. Trematode Mitochondrial Code</option> - <option value="22">22. Scenedesmus obliquus mitochondrial Code</option> - <option value="23">23. Thraustochytrium Mitochondrial Code</option> - <option value="24">24. Pterobranchia mitochondrial code</option> - </param> - <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> - <param name="matrix" type="select" label="Scoring matrix"> - <option value="BLOSUM90">BLOSUM90</option> - <option value="BLOSUM80">BLOSUM80</option> - <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> - <option value="BLOSUM50">BLOSUM50</option> - <option value="BLOSUM45">BLOSUM45</option> - <option value="PAM250">PAM250</option> - <option value="PAM70">PAM70</option> - <option value="PAM30">PAM30</option> - </param> - <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> - <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> - <validator type="in_range" min="0" /> - </param> - <!-- I'd like word_size to be optional, with minimum 2 for blastp --> - <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."> - <validator type="in_range" min="0" /> - </param> - <!-- - Can't use '-ungapped' on its own, error back is: - Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search - Tried using '-ungapped -comp_based_stats F' and tblastn crashed with 'Attempt to access NULL pointer.' - <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" /> - --> - <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/> - </when> - </conditional> - </inputs> - <outputs> - <data name="output1" format="tabular" label="tblastn on ${db_opts.db_opts_selector}"> - <change_format> - <when input="out_format" value="0" format="txt"/> - <when input="out_format" value="0 -html" format="html"/> - <when input="out_format" value="2" format="txt"/> - <when input="out_format" value="2 -html" format="html"/> - <when input="out_format" value="4" format="txt"/> - <when input="out_format" value="4 -html" format="html"/> - <when input="out_format" value="5" format="blastxml"/> - </change_format> - </data> - </outputs> - <requirements> - <requirement type="binary">tblastn</requirement> - </requirements> - <tests> - <test> - <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="database" value="" /> - <param name="evalue_cutoff" value="1e-10" /> - <param name="out_format" value="5" /> - <param name="adv_opts_selector" value="advanced" /> - <param name="filter_query" value="false" /> - <param name="matrix" value="BLOSUM80" /> - <param name="max_hits" value="0" /> - <param name="word_size" value="0" /> - <param name="parse_deflines" value="false" /> - <output name="output1" file="tblastn_four_human_vs_rhodopsin.xml" ftype="blastxml" /> - </test> - <test> - <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="database" value="" /> - <param name="evalue_cutoff" value="1e-10" /> - <param name="out_format" value="ext" /> - <param name="adv_opts_selector" value="advanced" /> - <param name="filter_query" value="false" /> - <param name="matrix" value="BLOSUM80" /> - <param name="max_hits" value="0" /> - <param name="word_size" value="0" /> - <param name="parse_deflines" value="false" /> - <output name="output1" file="tblastn_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" /> - </test> - <test> - <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="database" value="" /> - <param name="evalue_cutoff" value="1e-10" /> - <param name="out_format" value="6" /> - <param name="adv_opts_selector" value="advanced" /> - <param name="filter_query" value="false" /> - <param name="matrix" value="BLOSUM80" /> - <param name="max_hits" value="0" /> - <param name="word_size" value="0" /> - <param name="parse_deflines" value="false" /> - <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" /> - </test> - <test> - <!-- Same as above, but parse deflines - on BLAST 2.2.25+ makes no difference --> - <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="database" value="" /> - <param name="evalue_cutoff" value="1e-10" /> - <param name="out_format" value="6" /> - <param name="adv_opts_selector" value="advanced" /> - <param name="filter_query" value="false" /> - <param name="matrix" value="BLOSUM80" /> - <param name="max_hits" value="0" /> - <param name="word_size" value="0" /> - <param name="parse_deflines" value="true" /> - <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" /> - </test> - <test> - <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> - <param name="db_opts_selector" value="file" /> - <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> - <param name="database" value="" /> - <param name="evalue_cutoff" value="1e-10" /> - <param name="out_format" value="0 -html" /> - <param name="adv_opts_selector" value="advanced" /> - <param name="filter_query" value="false" /> - <param name="matrix" value="BLOSUM80" /> - <param name="max_hits" value="0" /> - <param name="word_size" value="0" /> - <param name="parse_deflines" value="false" /> - <output name="output1" file="tblastn_four_human_vs_rhodopsin.html" ftype="html" /> - </test> - </tests> - <help> - -.. class:: warningmark - -**Note**. Database searches may take a substantial amount of time. -For large input datasets it is advisable to allow overnight processing. - ------ - -**What it does** - -Search a *translated nucleotide database* using a *protein query*, -using the NCBI BLAST+ tblastn command line tool. - ------ - -**Output format** - -Because Galaxy focuses on processing tabular data, the default output of this -tool is tabular. The standard BLAST+ tabular output contains 12 columns: - -====== ========= ============================================ -Column NCBI name Description ------- --------- -------------------------------------------- - 1 qseqid Query Seq-id (ID of your sequence) - 2 sseqid Subject Seq-id (ID of the database hit) - 3 pident Percentage of identical matches - 4 length Alignment length - 5 mismatch Number of mismatches - 6 gapopen Number of gap openings - 7 qstart Start of alignment in query - 8 qend End of alignment in query - 9 sstart Start of alignment in subject (database hit) - 10 send End of alignment in subject (database hit) - 11 evalue Expectation value (E-value) - 12 bitscore Bit score -====== ========= ============================================ - -The BLAST+ tools can optionally output additional columns of information, -but this takes longer to calculate. Most (but not all) of these columns are -included by selecting the extended tabular output. The extra columns are -included *after* the standard 12 columns. This is so that you can write -workflow filtering steps that accept either the 12 or 24 column tabular -BLAST output. - -====== ============= =========================================== -Column NCBI name Description ------- ------------- ------------------------------------------- - 13 sallseqid All subject Seq-id(s), separated by a ';' - 14 score Raw score - 15 nident Number of identical matches - 16 positive Number of positive-scoring matches - 17 gaps Total number of gaps - 18 ppos Percentage of positive-scoring matches - 19 qframe Query frame - 20 sframe Subject frame - 21 qseq Aligned part of query sequence - 22 sseq Aligned part of subject sequence - 23 qlen Query sequence length - 24 slen Subject sequence length -====== ============= =========================================== - -The third option is BLAST XML output, which is designed to be parsed by -another program, and is understood by some Galaxy tools. - -You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). -The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. -The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. -The two query anchored outputs show a multiple sequence alignment between the query and all the matches, -and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). - -------- - -**References** - -Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. - - </help> -</tool>
--- a/ncbi_tblastx_wrapper.xml Thu Aug 23 07:32:06 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,252 +0,0 @@ -<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.12"> - <description>Search translated nucleotide database with translated nucleotide query sequence(s)</description> - <!-- If job splitting is enabled, break up the query file into parts --> - <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism> - <version_command>tblastx -version</version_command> - <command interpreter="python">hide_stderr.py -## The command is a Cheetah template which allows some Python based syntax. -## Lines starting hash hash are comments. Galaxy will turn newlines into spaces -tblastx --query "$query" -#if $db_opts.db_opts_selector == "db": - -db "${db_opts.database.fields.path}" -#else: - -subject "$db_opts.subject" -#end if --query_gencode $query_gencode --evalue $evalue_cutoff --out $output1 -##Set the extended list here so if/when we add things, saved workflows are not affected -#if str($out_format)=="ext": - -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" -#else: - -outfmt $out_format -#end if --num_threads 8 -#if $adv_opts.adv_opts_selector=="advanced": --db_gencode $adv_opts.db_gencode -$adv_opts.filter_query -$adv_opts.strand --matrix $adv_opts.matrix -## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string -## Note -max_target_seqs overrides -num_descriptions and -num_alignments -#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): --max_target_seqs $adv_opts.max_hits -#end if -#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): --word_size $adv_opts.word_size -#end if -$adv_opts.parse_deflines -## End of advanced options: -#end if - </command> - <inputs> - <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> - <conditional name="db_opts"> - <param name="db_opts_selector" type="select" label="Subject database/sequences"> - <option value="db" selected="True">BLAST Database</option> - <option value="file">FASTA file (pairwise e-values)</option> - </param> - <when value="db"> - <param name="database" type="select" label="Nucleotide BLAST database"> - <options from_file="blastdb.loc"> - <column name="value" index="0"/> - <column name="name" index="1"/> - <column name="path" index="2"/> - </options> - </param> - <param name="subject" type="hidden" value="" /> - </when> - <when value="file"> - <param name="database" type="hidden" value="" /> - <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> - </when> - </conditional> - <param name="query_gencode" type="select" label="Query genetic code"> - <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> - <option value="1" select="True">1. Standard</option> - <option value="2">2. Vertebrate Mitochondrial</option> - <option value="3">3. Yeast Mitochondrial</option> - <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> - <option value="5">5. Invertebrate Mitochondrial</option> - <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> - <option value="9">9. Echinoderm Mitochondrial</option> - <option value="10">10. Euplotid Nuclear</option> - <option value="11">11. Bacteria and Archaea</option> - <option value="12">12. Alternative Yeast Nuclear</option> - <option value="13">13. Ascidian Mitochondrial</option> - <option value="14">14. Flatworm Mitochondrial</option> - <option value="15">15. Blepharisma Macronuclear</option> - <option value="16">16. Chlorophycean Mitochondrial Code</option> - <option value="21">21. Trematode Mitochondrial Code</option> - <option value="22">22. Scenedesmus obliquus mitochondrial Code</option> - <option value="23">23. Thraustochytrium Mitochondrial Code</option> - <option value="24">24. Pterobranchia mitochondrial code</option> - </param> - <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> - <param name="out_format" type="select" label="Output format"> - <option value="6" selected="True">Tabular (standard 12 columns)</option> - <option value="ext">Tabular (extended 24 columns)</option> - <option value="5">BLAST XML</option> - <option value="0">Pairwise text</option> - <option value="0 -html">Pairwise HTML</option> - <option value="2">Query-anchored text</option> - <option value="2 -html">Query-anchored HTML</option> - <option value="4">Flat query-anchored text</option> - <option value="4 -html">Flat query-anchored HTML</option> - <!-- - <option value="-outfmt 11">BLAST archive format (ASN.1)</option> - --> - </param> - <conditional name="adv_opts"> - <param name="adv_opts_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic" /> - <when value="advanced"> - <param name="db_gencode" type="select" label="Database/subject genetic code"> - <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> - <option value="1" select="True">1. Standard</option> - <option value="2">2. Vertebrate Mitochondrial</option> - <option value="3">3. Yeast Mitochondrial</option> - <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> - <option value="5">5. Invertebrate Mitochondrial</option> - <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> - <option value="9">9. Echinoderm Mitochondrial</option> - <option value="10">10. Euplotid Nuclear</option> - <option value="11">11. Bacteria and Archaea</option> - <option value="12">12. Alternative Yeast Nuclear</option> - <option value="13">13. Ascidian Mitochondrial</option> - <option value="14">14. Flatworm Mitochondrial</option> - <option value="15">15. Blepharisma Macronuclear</option> - <option value="16">16. Chlorophycean Mitochondrial Code</option> - <option value="21">21. Trematode Mitochondrial Code</option> - <option value="22">22. Scenedesmus obliquus mitochondrial Code</option> - <option value="23">23. Thraustochytrium Mitochondrial Code</option> - <option value="24">24. Pterobranchia mitochondrial code</option> - </param> - <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> - <param name="strand" type="select" label="Query strand(s) to search against database/subject"> - <option value="-strand both">Both</option> - <option value="-strand plus">Plus (forward)</option> - <option value="-strand minus">Minus (reverse complement)</option> - </param> - <param name="matrix" type="select" label="Scoring matrix"> - <option value="BLOSUM90">BLOSUM90</option> - <option value="BLOSUM80">BLOSUM80</option> - <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> - <option value="BLOSUM50">BLOSUM50</option> - <option value="BLOSUM45">BLOSUM45</option> - <option value="PAM250">PAM250</option> - <option value="PAM70">PAM70</option> - <option value="PAM30">PAM30</option> - </param> - <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> - <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> - <validator type="in_range" min="0" /> - </param> - <!-- I'd like word_size to be optional, with minimum 2 for tblastx --> - <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."> - <validator type="in_range" min="0" /> - </param> - <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/> - </when> - </conditional> - </inputs> - <outputs> - <data name="output1" format="tabular" label="tblastx on ${db_opts.db_opts_selector}"> - <change_format> - <when input="out_format" value="0" format="txt"/> - <when input="out_format" value="0 -html" format="html"/> - <when input="out_format" value="2" format="txt"/> - <when input="out_format" value="2 -html" format="html"/> - <when input="out_format" value="4" format="txt"/> - <when input="out_format" value="4 -html" format="html"/> - <when input="out_format" value="5" format="blastxml"/> - </change_format> - </data> - </outputs> - <requirements> - <requirement type="binary">tblastx</requirement> - </requirements> - <help> - -.. class:: warningmark - -**Note**. Database searches may take a substantial amount of time. -For large input datasets it is advisable to allow overnight processing. - ------ - -**What it does** - -Search a *translated nucleotide database* using a *protein query*, -using the NCBI BLAST+ tblastx command line tool. - ------ - -**Output format** - -Because Galaxy focuses on processing tabular data, the default output of this -tool is tabular. The standard BLAST+ tabular output contains 12 columns: - -====== ========= ============================================ -Column NCBI name Description ------- --------- -------------------------------------------- - 1 qseqid Query Seq-id (ID of your sequence) - 2 sseqid Subject Seq-id (ID of the database hit) - 3 pident Percentage of identical matches - 4 length Alignment length - 5 mismatch Number of mismatches - 6 gapopen Number of gap openings - 7 qstart Start of alignment in query - 8 qend End of alignment in query - 9 sstart Start of alignment in subject (database hit) - 10 send End of alignment in subject (database hit) - 11 evalue Expectation value (E-value) - 12 bitscore Bit score -====== ========= ============================================ - -The BLAST+ tools can optionally output additional columns of information, -but this takes longer to calculate. Most (but not all) of these columns are -included by selecting the extended tabular output. The extra columns are -included *after* the standard 12 columns. This is so that you can write -workflow filtering steps that accept either the 12 or 24 column tabular -BLAST output. - -====== ============= =========================================== -Column NCBI name Description ------- ------------- ------------------------------------------- - 13 sallseqid All subject Seq-id(s), separated by a ';' - 14 score Raw score - 15 nident Number of identical matches - 16 positive Number of positive-scoring matches - 17 gaps Total number of gaps - 18 ppos Percentage of positive-scoring matches - 19 qframe Query frame - 20 sframe Subject frame - 21 qseq Aligned part of query sequence - 22 sseq Aligned part of subject sequence - 23 qlen Query sequence length - 24 slen Subject sequence length -====== ============= =========================================== - -The third option is BLAST XML output, which is designed to be parsed by -another program, and is understood by some Galaxy tools. - -You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). -The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. -The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. -The two query anchored outputs show a multiple sequence alignment between the query and all the matches, -and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). - -------- - -**References** - -Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. - - </help> -</tool>
--- a/tool_dependencies.xml Thu Aug 23 07:32:06 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="blast+" version="2.2.26+"> - <install version="1.0"> - <actions> - <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-src.tar.gz</action> - <action type="shell_command">cd c++ && ./configure --prefix=$INSTALL_DIR && make && make install</action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> -These links provide information for building the NCBI Blast+ package in most environments. - -System requirements -http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download - </readme> - </package> -</tool_dependency> -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/blastdb.loc.sample Thu Aug 23 09:00:40 2012 -0400 @@ -0,0 +1,38 @@ +#This is a sample file distributed with Galaxy that is used to define a +#list of nucleotide BLAST databases, using three columns tab separated +#(longer whitespace are TAB characters): +# +#<unique_id> <database_caption> <base_name_path> +# +#The captions typically contain spaces and might end with the build date. +#It is important that the actual database name does not have a space in it, +#and that the first tab that appears in the line is right before the path. +# +#So, for example, if your database is nt and the path to your base name +#is /depot/data2/galaxy/blastdb/nt/nt.chunk, then the blastdb.loc entry +#would look like this: +# +#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk +# +#and your /depot/data2/galaxy/blastdb/nt directory would contain all of +#your "base names" (e.g.): +# +#-rw-r--r-- 1 wychung galaxy 23437408 2008-04-09 11:26 nt.chunk.00.nhr +#-rw-r--r-- 1 wychung galaxy 3689920 2008-04-09 11:26 nt.chunk.00.nin +#-rw-r--r-- 1 wychung galaxy 251215198 2008-04-09 11:26 nt.chunk.00.nsq +#...etc... +# +#Your blastdb.loc file should include an entry per line for each "base name" +#you have stored. For example: +# +#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk +#wgs_30_Nov_2009 wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk +#test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test +#...etc... +# +#See also blastdb_p.loc which is for any protein BLAST database. +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. +#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/blastdb_p.loc.sample Thu Aug 23 09:00:40 2012 -0400 @@ -0,0 +1,27 @@ +#This is a sample file distributed with Galaxy that is used to define a +#list of protein BLAST databases, using three columns tab separated +#(longer whitespace are TAB characters): +# +#<unique_id> <database_caption> <base_name_path> +# +#The captions typically contain spaces and might end with the build date. +#It is important that the actual database name does not have a space in it, +#and that the first tab that appears in the line is right before the path. +# +#So, for example, if your database is NR and the path to your base name +#is /data/blastdb/nr, then the blastdb_p.loc entry would look like this: +# +#nr NCBI NR (non redundant) /data/blastdb/nr +# +#and your /data/blastdb directory would contain all of the files associated +#with the database, /data/blastdb/nr.*. +# +#Your blastdb_p.loc file should include an entry per line for each "base name" +#you have stored. For example: +# +#nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr +#nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr +#...etc... +# +#See also blastdb.loc which is for any nucleotide BLAST database. +#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py Thu Aug 23 09:00:40 2012 -0400 @@ -0,0 +1,254 @@ +#!/usr/bin/env python +"""Convert a BLAST XML file to 12 column tabular output + +Takes three command line options, input BLAST XML filename, output tabular +BLAST filename, output format (std for standard 12 columns, or ext for the +extended 24 columns offered in the BLAST+ wrappers). + +The 12 columns output are 'qseqid sseqid pident length mismatch gapopen qstart +qend sstart send evalue bitscore' or 'std' at the BLAST+ command line, which +mean: + +====== ========= ============================================ +Column NCBI name Description +------ --------- -------------------------------------------- + 1 qseqid Query Seq-id (ID of your sequence) + 2 sseqid Subject Seq-id (ID of the database hit) + 3 pident Percentage of identical matches + 4 length Alignment length + 5 mismatch Number of mismatches + 6 gapopen Number of gap openings + 7 qstart Start of alignment in query + 8 qend End of alignment in query + 9 sstart Start of alignment in subject (database hit) + 10 send End of alignment in subject (database hit) + 11 evalue Expectation value (E-value) + 12 bitscore Bit score +====== ========= ============================================ + +The additional columns offered in the Galaxy BLAST+ wrappers are: + +====== ============= =========================================== +Column NCBI name Description +------ ------------- ------------------------------------------- + 13 sallseqid All subject Seq-id(s), separated by a ';' + 14 score Raw score + 15 nident Number of identical matches + 16 positive Number of positive-scoring matches + 17 gaps Total number of gaps + 18 ppos Percentage of positive-scoring matches + 19 qframe Query frame + 20 sframe Subject frame + 21 qseq Aligned part of query sequence + 22 sseq Aligned part of subject sequence + 23 qlen Query sequence length + 24 slen Subject sequence length +====== ============= =========================================== + +Most of these fields are given explicitly in the XML file, others some like +the percentage identity and the number of gap openings must be calculated. + +Be aware that the sequence in the extended tabular output or XML direct from +BLAST+ may or may not use XXXX masking on regions of low complexity. This +can throw the off the calculation of percentage identity and gap openings. +[In fact, both BLAST 2.2.24+ and 2.2.25+ have a subtle bug in this regard, +with these numbers changing depending on whether or not the low complexity +filter is used.] + +This script attempts to produce identical output to what BLAST+ would have done. +However, check this with "diff -b ..." since BLAST+ sometimes includes an extra +space character (probably a bug). +""" +import sys +import re + +if sys.version_info[:2] >= ( 2, 5 ): + import xml.etree.cElementTree as ElementTree +else: + from galaxy import eggs + import pkg_resources; pkg_resources.require( "elementtree" ) + from elementtree import ElementTree + +def stop_err( msg ): + sys.stderr.write("%s\n" % msg) + sys.exit(1) + +#Parse Command Line +try: + in_file, out_file, out_fmt = sys.argv[1:] +except: + stop_err("Expect 3 arguments: input BLAST XML file, output tabular file, out format (std or ext)") + +if out_fmt == "std": + extended = False +elif out_fmt == "x22": + stop_err("Format argument x22 has been replaced with ext (extended 24 columns)") +elif out_fmt == "ext": + extended = True +else: + stop_err("Format argument should be std (12 column) or ext (extended 24 columns)") + + +# get an iterable +try: + context = ElementTree.iterparse(in_file, events=("start", "end")) +except: + stop_err("Invalid data format.") +# turn it into an iterator +context = iter(context) +# get the root element +try: + event, root = context.next() +except: + stop_err( "Invalid data format." ) + + +re_default_query_id = re.compile("^Query_\d+$") +assert re_default_query_id.match("Query_101") +assert not re_default_query_id.match("Query_101a") +assert not re_default_query_id.match("MyQuery_101") +re_default_subject_id = re.compile("^Subject_\d+$") +assert re_default_subject_id.match("Subject_1") +assert not re_default_subject_id.match("Subject_") +assert not re_default_subject_id.match("Subject_12a") +assert not re_default_subject_id.match("TheSubject_1") + + +outfile = open(out_file, 'w') +blast_program = None +for event, elem in context: + if event == "end" and elem.tag == "BlastOutput_program": + blast_program = elem.text + # for every <Iteration> tag + if event == "end" and elem.tag == "Iteration": + #Expecting either this, from BLAST 2.2.25+ using FASTA vs FASTA + # <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID> + # <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def> + # <Iteration_query-len>406</Iteration_query-len> + # <Iteration_hits></Iteration_hits> + # + #Or, from BLAST 2.2.24+ run online + # <Iteration_query-ID>Query_1</Iteration_query-ID> + # <Iteration_query-def>Sample</Iteration_query-def> + # <Iteration_query-len>516</Iteration_query-len> + # <Iteration_hits>... + qseqid = elem.findtext("Iteration_query-ID") + if re_default_query_id.match(qseqid): + #Place holder ID, take the first word of the query definition + qseqid = elem.findtext("Iteration_query-def").split(None,1)[0] + qlen = int(elem.findtext("Iteration_query-len")) + + # for every <Hit> within <Iteration> + for hit in elem.findall("Iteration_hits/Hit"): + #Expecting either this, + # <Hit_id>gi|3024260|sp|P56514.1|OPSD_BUFBU</Hit_id> + # <Hit_def>RecName: Full=Rhodopsin</Hit_def> + # <Hit_accession>P56514</Hit_accession> + #or, + # <Hit_id>Subject_1</Hit_id> + # <Hit_def>gi|57163783|ref|NP_001009242.1| rhodopsin [Felis catus]</Hit_def> + # <Hit_accession>Subject_1</Hit_accession> + # + #apparently depending on the parse_deflines switch + sseqid = hit.findtext("Hit_id").split(None,1)[0] + hit_def = sseqid + " " + hit.findtext("Hit_def") + if re_default_subject_id.match(sseqid) \ + and sseqid == hit.findtext("Hit_accession"): + #Place holder ID, take the first word of the subject definition + hit_def = hit.findtext("Hit_def") + sseqid = hit_def.split(None,1)[0] + # for every <Hsp> within <Hit> + for hsp in hit.findall("Hit_hsps/Hsp"): + nident = hsp.findtext("Hsp_identity") + length = hsp.findtext("Hsp_align-len") + pident = "%0.2f" % (100*float(nident)/float(length)) + + q_seq = hsp.findtext("Hsp_qseq") + h_seq = hsp.findtext("Hsp_hseq") + m_seq = hsp.findtext("Hsp_midline") + assert len(q_seq) == len(h_seq) == len(m_seq) == int(length) + gapopen = str(len(q_seq.replace('-', ' ').split())-1 + \ + len(h_seq.replace('-', ' ').split())-1) + + mismatch = m_seq.count(' ') + m_seq.count('+') \ + - q_seq.count('-') - h_seq.count('-') + #TODO - Remove this alternative mismatch calculation and test + #once satisifed there are no problems + expected_mismatch = len(q_seq) \ + - sum(1 for q,h in zip(q_seq, h_seq) \ + if q == h or q == "-" or h == "-") + xx = sum(1 for q,h in zip(q_seq, h_seq) if q=="X" and h=="X") + if not (expected_mismatch - q_seq.count("X") <= int(mismatch) <= expected_mismatch + xx): + stop_err("%s vs %s mismatches, expected %i <= %i <= %i" \ + % (qseqid, sseqid, expected_mismatch - q_seq.count("X"), + int(mismatch), expected_mismatch)) + + #TODO - Remove this alternative identity calculation and test + #once satisifed there are no problems + expected_identity = sum(1 for q,h in zip(q_seq, h_seq) if q == h) + if not (expected_identity - xx <= int(nident) <= expected_identity + q_seq.count("X")): + stop_err("%s vs %s identities, expected %i <= %i <= %i" \ + % (qseqid, sseqid, expected_identity, int(nident), + expected_identity + q_seq.count("X"))) + + + evalue = hsp.findtext("Hsp_evalue") + if evalue == "0": + evalue = "0.0" + else: + evalue = "%0.0e" % float(evalue) + + bitscore = float(hsp.findtext("Hsp_bit-score")) + if bitscore < 100: + #Seems to show one decimal place for lower scores + bitscore = "%0.1f" % bitscore + else: + #Note BLAST does not round to nearest int, it truncates + bitscore = "%i" % bitscore + + values = [qseqid, + sseqid, + pident, + length, #hsp.findtext("Hsp_align-len") + str(mismatch), + gapopen, + hsp.findtext("Hsp_query-from"), #qstart, + hsp.findtext("Hsp_query-to"), #qend, + hsp.findtext("Hsp_hit-from"), #sstart, + hsp.findtext("Hsp_hit-to"), #send, + evalue, #hsp.findtext("Hsp_evalue") in scientific notation + bitscore, #hsp.findtext("Hsp_bit-score") rounded + ] + + if extended: + sallseqid = ";".join(name.split(None,1)[0] for name in hit_def.split(">")) + #print hit_def, "-->", sallseqid + positive = hsp.findtext("Hsp_positive") + ppos = "%0.2f" % (100*float(positive)/float(length)) + qframe = hsp.findtext("Hsp_query-frame") + sframe = hsp.findtext("Hsp_hit-frame") + if blast_program == "blastp": + #Probably a bug in BLASTP that they use 0 or 1 depending on format + if qframe == "0": qframe = "1" + if sframe == "0": sframe = "1" + slen = int(hit.findtext("Hit_len")) + values.extend([sallseqid, + hsp.findtext("Hsp_score"), #score, + nident, + positive, + hsp.findtext("Hsp_gaps"), #gaps, + ppos, + qframe, + sframe, + #NOTE - for blastp, XML shows original seq, tabular uses XXX masking + q_seq, + h_seq, + str(qlen), + str(slen), + ]) + #print "\t".join(values) + outfile.write("\t".join(values) + "\n") + # prevents ElementTree from growing large datastructure + root.clear() + elem.clear() +outfile.close()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.xml Thu Aug 23 09:00:40 2012 -0400 @@ -0,0 +1,127 @@ +<tool id="blastxml_to_tabular" name="BLAST XML to tabular" version="0.0.8"> + <description>Convert BLAST XML output to tabular</description> + <command interpreter="python"> + blastxml_to_tabular.py $blastxml_file $tabular_file $out_format + </command> + <inputs> + <param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/> + <param name="out_format" type="select" label="Output format"> + <option value="std" selected="True">Tabular (standard 12 columns)</option> + <option value="ext">Tabular (extended 24 columns)</option> + </param> + </inputs> + <outputs> + <data name="tabular_file" format="tabular" label="BLAST results as tabular" /> + </outputs> + <requirements> + </requirements> + <tests> + <test> + <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> + <param name="out_format" value="std" /> + <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin.tabluar --> + <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted.tabular" ftype="tabular" /> + </test> + <test> + <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> + <param name="out_format" value="ext" /> + <!-- Note this has some white space differences from the actual blastp output blast_four_human_vs_rhodopsin_22c.tabluar --> + <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_converted_ext.tabular" ftype="tabular" /> + </test> + <test> + <param name="blastxml_file" value="blastp_sample.xml" ftype="blastxml" /> + <param name="out_format" value="std" /> + <!-- Note this has some white space differences from the actual blastp output --> + <output name="tabular_file" file="blastp_sample_converted.tabular" ftype="tabular" /> + </test> + <test> + <param name="blastxml_file" value="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" /> + <param name="out_format" value="std" /> + <!-- Note this has some white space differences from the actual blastx output --> + <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted.tabular" ftype="tabular" /> + </test> + <test> + <param name="blastxml_file" value="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" /> + <param name="out_format" value="ext" /> + <!-- Note this has some white space and XXXX masking differences from the actual blastx output --> + <output name="tabular_file" file="blastx_rhodopsin_vs_four_human_converted_ext.tabular" ftype="tabular" /> + </test> + <test> + <param name="blastxml_file" value="blastx_sample.xml" ftype="blastxml" /> + <param name="out_format" value="std" /> + <!-- Note this has some white space differences from the actual blastx output --> + <output name="tabular_file" file="blastx_sample_converted.tabular" ftype="tabular" /> + </test> + <test> + <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" /> + <param name="out_format" value="std" /> + <!-- Note this has some white space differences from the actual blastp output --> + <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_std.tabular" ftype="tabular" /> + </test> + <test> + <param name="blastxml_file" value="blastp_human_vs_pdb_seg_no.xml" ftype="blastxml" /> + <param name="out_format" value="ext" /> + <!-- Note this has some white space differences from the actual blastp output --> + <output name="tabular_file" file="blastp_human_vs_pdb_seg_no_converted_ext.tabular" ftype="tabular" /> + </test> + </tests> + <help> + +**What it does** + +NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of +formats including tabular and a more detailed XML format. A complex workflow +may need both the XML and the tabular output - but running BLAST twice is +slow and wasteful. + +This tool takes the BLAST XML output and by default converts it into the +standard 12 column tabular equivalent: + +====== ========= ============================================ +Column NCBI name Description +------ --------- -------------------------------------------- + 1 qseqid Query Seq-id (ID of your sequence) + 2 sseqid Subject Seq-id (ID of the database hit) + 3 pident Percentage of identical matches + 4 length Alignment length + 5 mismatch Number of mismatches + 6 gapopen Number of gap openings + 7 qstart Start of alignment in query + 8 qend End of alignment in query + 9 sstart Start of alignment in subject (database hit) + 10 send End of alignment in subject (database hit) + 11 evalue Expectation value (E-value) + 12 bitscore Bit score +====== ========= ============================================ + +The BLAST+ tools can optionally output additional columns of information, +but this takes longer to calculate. Most (but not all) of these columns are +included by selecting the extended tabular output. The extra columns are +included *after* the standard 12 columns. This is so that you can write +workflow filtering steps that accept either the 12 or 22 column tabular +BLAST output. + +====== ============= =========================================== +Column NCBI name Description +------ ------------- ------------------------------------------- + 13 sallseqid All subject Seq-id(s), separated by a ';' + 14 score Raw score + 15 nident Number of identical matches + 16 positive Number of positive-scoring matches + 17 gaps Total number of gaps + 18 ppos Percentage of positive-scoring matches + 19 qframe Query frame + 20 sframe Subject frame + 21 qseq Aligned part of query sequence + 22 sseq Aligned part of subject sequence + 23 qlen Query sequence length + 24 slen Subject sequence length +====== ============= =========================================== + +Beware that the XML file (and thus the conversion) and the tabular output +direct from BLAST+ may differ in the presence of XXXX masking on regions +low complexity (columns 21 and 22), and thus also calculated figures like +the percentage idenity (column 3). + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/hide_stderr.py Thu Aug 23 09:00:40 2012 -0400 @@ -0,0 +1,49 @@ +#!/usr/bin/env python +"""A simple script to redirect stderr to stdout when the return code is zero. + +See https://bitbucket.org/galaxy/galaxy-central/issue/325/ + +Currently Galaxy ignores the return code from command line tools (even if it +is non-zero which by convention indicates an error) and treats any output on +stderr as an error (even though by convention stderr is used for errors or +warnings). + +This script runs the given command line, capturing all stdout and stderr in +memory, and gets the return code. For a zero return code, any stderr (which +should be warnings only) is added to the stdout. That way Galaxy believes +everything is fine. For a non-zero return code, we output stdout as is, and +any stderr, plus the return code to ensure there is some output on stderr. +That way Galaxy treats this as an error. + +Once issue 325 is fixed, this script will not be needed. +""" +import sys +import subprocess + +#Avoid using shell=True when we call subprocess to ensure if the Python +#script is killed, so too is the BLAST process. +try: + words = [] + for w in sys.argv[1:]: + if " " in w: + words.append('"%s"' % w) + else: + words.append(w) + cmd = " ".join(words) + child = subprocess.Popen(sys.argv[1:], + stdout=subprocess.PIPE, stderr=subprocess.PIPE) +except Exception, err: + sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err)) + sys.exit(1) +#Use .communicate as can get deadlocks with .wait(), +stdout, stderr = child.communicate() +return_code = child.returncode + +if return_code: + sys.stdout.write(stdout) + sys.stderr.write(stderr) + sys.stderr.write("Return error code %i from command:\n" % return_code) + sys.stderr.write("%s\n" % cmd) +else: + sys.stdout.write(stdout) + sys.stdout.write(stderr)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blast_plus.txt Thu Aug 23 09:00:40 2012 -0400 @@ -0,0 +1,81 @@ +Galaxy wrappers for NCBI BLAST+ suite +===================================== + +These wrappers are copyright 2010-2012 by Peter Cock, The James Hutton Institute +(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. +See the licence text below. + +Currently tested with NCBI BLAST 2.2.26+ (i.e. version 2.2.26 of BLAST+), +and do not work with the NCBI 'legacy' BLAST suite (e.g. blastall). + +Note that these wrappers were originally distributed as part of the main +Galaxy repository, but as of August 2012 moved to the Galaxy Tool Shed. +My thanks to Dannon Baker from the Galaxy development team for this assistance +with this. + + +Manual Installation +=================== + +For those not using Galaxy's automated installation from the Tool Shed, put +the XML and Python files under tools/ncbi_blast_plus and add the XML files +to your tool_conf.xml as normal. + +You must tell Galaxy about any system level BLAST databases using configuration +files blastdb.loc (nucleotide databases like NT) and blastdb_p.loc (protein +databases like NR). + +You will also need to install the 'blast_datatypes' from the Tool Shed. This +defines the BLAST XML file format ('blastxml'). + + +History +======= + +v0.0.11 - Final revision as part of the Galaxy main repository, and the + first release via the Tool Shed +v0.0.12 - Implements genetic code option for translation searches. + - Changes <parallelism> to 1000 sequences at a time (to cope with + very large sets of queries where BLAST+ can become memory hungry) + - Include warning that BLAST+ with subject FASTA gives pairwise + e-values + + +Developers +========== + +This script and related tools are being developed on the following hg branch: +http://bitbucket.org/peterjc/galaxy-central/src/tools + +For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball I use +the following command from the Galaxy root folder: + +$ ./tools/ncbi_blast_plus/make_ncbi_blast_plus.sh + +This similifies ensuring a consistent set of files is bundled each time, +including all the relevant test files. + + +Licence (MIT/BSD style) +======================= + +Permission to use, copy, modify, and distribute this software and its +documentation with or without modifications and for any purpose and +without fee is hereby granted, provided that any copyright notices +appear in all copies and that both those copyright notices and this +permission notice appear in supporting documentation, and that the +names of the contributors or copyright holders not be used in +advertising or publicity pertaining to distribution of the software +without specific prior permission. + +THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +OR PERFORMANCE OF THIS SOFTWARE. + +NOTE: This is the licence for the Galaxy Wrapper only. BLAST+ and +associated data files are available and licenced separately.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Thu Aug 23 09:00:40 2012 -0400 @@ -0,0 +1,211 @@ +<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.12"> + <description>Search nucleotide database with nucleotide query sequence(s)</description> + <!-- If job splitting is enabled, break up the query file into parts --> + <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism> + <version_command>blastn -version</version_command> + <command interpreter="python">hide_stderr.py +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +blastn +-query "$query" +#if $db_opts.db_opts_selector == "db": + -db "${db_opts.database.fields.path}" +#else: + -subject "$db_opts.subject" +#end if +-task $blast_type +-evalue $evalue_cutoff +-out $output1 +##Set the extended list here so if/when we add things, saved workflows are not affected +#if str($out_format)=="ext": + -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" +#else: + -outfmt $out_format +#end if +-num_threads 8 +#if $adv_opts.adv_opts_selector=="advanced": +$adv_opts.filter_query +$adv_opts.strand +## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string +## Note -max_target_seqs overrides -num_descriptions and -num_alignments +#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): +-max_target_seqs $adv_opts.max_hits +#end if +#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): +-word_size $adv_opts.word_size +#end if +$adv_opts.ungapped +$adv_opts.parse_deflines +## End of advanced options: +#end if + </command> + <inputs> + <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="True">BLAST Database</option> + <option value="file">FASTA file (pairwise e-values)</option> + </param> + <when value="db"> + <param name="database" type="select" label="Nucleotide BLAST database"> + <options from_file="blastdb.loc"> + <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="path" index="2"/> + </options> + </param> + <param name="subject" type="hidden" value="" /> + </when> + <when value="file"> + <param name="database" type="hidden" value="" /> + <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> + </when> + </conditional> + <param name="blast_type" type="select" display="radio" label="Type of BLAST"> + <option value="megablast">megablast</option> + <option value="blastn">blastn</option> + <option value="blastn-short">blastn-short</option> + <option value="dc-megablast">dc-megablast</option> + <!-- Using BLAST 2.2.24+ this gives an error: + BLAST engine error: Program type 'vecscreen' not supported + <option value="vecscreen">vecscreen</option> + --> + </param> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> + <param name="out_format" type="select" label="Output format"> + <option value="6" selected="True">Tabular (standard 12 columns)</option> + <option value="ext">Tabular (extended 24 columns)</option> + <option value="5">BLAST XML</option> + <option value="0">Pairwise text</option> + <option value="0 -html">Pairwise HTML</option> + <option value="2">Query-anchored text</option> + <option value="2 -html">Query-anchored HTML</option> + <option value="4">Flat query-anchored text</option> + <option value="4 -html">Flat query-anchored HTML</option> + <!-- + <option value="-outfmt 11">BLAST archive format (ASN.1)</option> + --> + </param> + <conditional name="adv_opts"> + <param name="adv_opts_selector" type="select" label="Advanced Options"> + <option value="basic" selected="True">Hide Advanced Options</option> + <option value="advanced">Show Advanced Options</option> + </param> + <when value="basic" /> + <when value="advanced"> + <!-- Could use a select (yes, no, other) where other allows setting 'level window linker' --> + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" /> + <param name="strand" type="select" label="Query strand(s) to search against database/subject"> + <option value="-strand both">Both</option> + <option value="-strand plus">Plus (forward)</option> + <option value="-strand minus">Minus (reverse complement)</option> + </param> + <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> + <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param> + <!-- I'd like word_size to be optional, with minimum 4 for blastn --> + <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4."> + <validator type="in_range" min="0" /> + </param> + <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> + <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/> + </when> + </conditional> + </inputs> + <outputs> + <data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}"> + <change_format> + <when input="out_format" value="0" format="txt"/> + <when input="out_format" value="0 -html" format="html"/> + <when input="out_format" value="2" format="txt"/> + <when input="out_format" value="2 -html" format="html"/> + <when input="out_format" value="4" format="txt"/> + <when input="out_format" value="4 -html" format="html"/> + <when input="out_format" value="5" format="blastxml"/> + </change_format> + </data> + </outputs> + <requirements> + <requirement type="binary">blastn</requirement> + </requirements> + <help> + +.. class:: warningmark + +**Note**. Database searches may take a substantial amount of time. +For large input datasets it is advisable to allow overnight processing. + +----- + +**What it does** + +Search a *nucleotide database* using a *nucleotide query*, +using the NCBI BLAST+ blastn command line tool. +Algorithms include blastn, megablast, and discontiguous megablast. + +----- + +**Output format** + +Because Galaxy focuses on processing tabular data, the default output of this +tool is tabular. The standard BLAST+ tabular output contains 12 columns: + +====== ========= ============================================ +Column NCBI name Description +------ --------- -------------------------------------------- + 1 qseqid Query Seq-id (ID of your sequence) + 2 sseqid Subject Seq-id (ID of the database hit) + 3 pident Percentage of identical matches + 4 length Alignment length + 5 mismatch Number of mismatches + 6 gapopen Number of gap openings + 7 qstart Start of alignment in query + 8 qend End of alignment in query + 9 sstart Start of alignment in subject (database hit) + 10 send End of alignment in subject (database hit) + 11 evalue Expectation value (E-value) + 12 bitscore Bit score +====== ========= ============================================ + +The BLAST+ tools can optionally output additional columns of information, +but this takes longer to calculate. Most (but not all) of these columns are +included by selecting the extended tabular output. The extra columns are +included *after* the standard 12 columns. This is so that you can write +workflow filtering steps that accept either the 12 or 24 column tabular +BLAST output. + +====== ============= =========================================== +Column NCBI name Description +------ ------------- ------------------------------------------- + 13 sallseqid All subject Seq-id(s), separated by a ';' + 14 score Raw score + 15 nident Number of identical matches + 16 positive Number of positive-scoring matches + 17 gaps Total number of gaps + 18 ppos Percentage of positive-scoring matches + 19 qframe Query frame + 20 sframe Subject frame + 21 qseq Aligned part of query sequence + 22 sseq Aligned part of subject sequence + 23 qlen Query sequence length + 24 slen Subject sequence length +====== ============= =========================================== + +The third option is BLAST XML output, which is designed to be parsed by +another program, and is understood by some Galaxy tools. + +You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). +The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. +The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. +The two query anchored outputs show a multiple sequence alignment between the query and all the matches, +and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). + +------- + +**References** + +Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214. + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Thu Aug 23 09:00:40 2012 -0400 @@ -0,0 +1,278 @@ +<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.12"> + <description>Search protein database with protein query sequence(s)</description> + <!-- If job splitting is enabled, break up the query file into parts --> + <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism> + <version_command>blastp -version</version_command> + <command interpreter="python">hide_stderr.py +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +blastp +-query "$query" +#if $db_opts.db_opts_selector == "db": + -db "${db_opts.database.fields.path}" +#else: + -subject "$db_opts.subject" +#end if +-task $blast_type +-evalue $evalue_cutoff +-out $output1 +##Set the extended list here so if/when we add things, saved workflows are not affected +#if str($out_format)=="ext": + -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" +#else: + -outfmt $out_format +#end if +-num_threads 8 +#if $adv_opts.adv_opts_selector=="advanced": +$adv_opts.filter_query +-matrix $adv_opts.matrix +## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string +## Note -max_target_seqs overrides -num_descriptions and -num_alignments +#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): +-max_target_seqs $adv_opts.max_hits +#end if +#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): +-word_size $adv_opts.word_size +#end if +##Ungapped disabled for now - see comments below +##$adv_opts.ungapped +$adv_opts.parse_deflines +## End of advanced options: +#end if + </command> + <inputs> + <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="True">BLAST Database</option> + <option value="file">FASTA file (pairwise e-values)</option> + </param> + <when value="db"> + <param name="database" type="select" label="Protein BLAST database"> + <options from_file="blastdb_p.loc"> + <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="path" index="2"/> + </options> + </param> + <param name="subject" type="hidden" value="" /> + </when> + <when value="file"> + <param name="database" type="hidden" value="" /> + <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> + </when> + </conditional> + <param name="blast_type" type="select" display="radio" label="Type of BLAST"> + <option value="blastp">blastp</option> + <option value="blastp-short">blastp-short</option> + </param> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> + <param name="out_format" type="select" label="Output format"> + <option value="6" selected="True">Tabular (standard 12 columns)</option> + <option value="ext">Tabular (extended 24 columns)</option> + <option value="5">BLAST XML</option> + <option value="0">Pairwise text</option> + <option value="0 -html">Pairwise HTML</option> + <option value="2">Query-anchored text</option> + <option value="2 -html">Query-anchored HTML</option> + <option value="4">Flat query-anchored text</option> + <option value="4 -html">Flat query-anchored HTML</option> + <!-- + <option value="-outfmt 11">BLAST archive format (ASN.1)</option> + --> + </param> + <conditional name="adv_opts"> + <param name="adv_opts_selector" type="select" label="Advanced Options"> + <option value="basic" selected="True">Hide Advanced Options</option> + <option value="advanced">Show Advanced Options</option> + </param> + <when value="basic" /> + <when value="advanced"> + <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" /> + <param name="matrix" type="select" label="Scoring matrix"> + <option value="BLOSUM90">BLOSUM90</option> + <option value="BLOSUM80">BLOSUM80</option> + <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> + <option value="BLOSUM50">BLOSUM50</option> + <option value="BLOSUM45">BLOSUM45</option> + <option value="PAM250">PAM250</option> + <option value="PAM70">PAM70</option> + <option value="PAM30">PAM30</option> + </param> + <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> + <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param> + <!-- I'd like word_size to be optional, with minimum 2 for blastp --> + <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."> + <validator type="in_range" min="0" /> + </param> + <!-- + Can't use '-ungapped' on its own, error back is: + Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search + Tried using '-ungapped -comp_based_stats F' and blastp crashed with 'Attempt to access NULL pointer.' + <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" /> + --> + <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/> + </when> + </conditional> + </inputs> + <outputs> + <data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}"> + <change_format> + <when input="out_format" value="0" format="txt"/> + <when input="out_format" value="0 -html" format="html"/> + <when input="out_format" value="2" format="txt"/> + <when input="out_format" value="2 -html" format="html"/> + <when input="out_format" value="4" format="txt"/> + <when input="out_format" value="4 -html" format="html"/> + <when input="out_format" value="5" format="blastxml"/> + </change_format> + </data> + </outputs> + <requirements> + <requirement type="binary">blastp</requirement> + </requirements> + <tests> + <test> + <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> + <param name="database" value="" /> + <param name="evalue_cutoff" value="1e-8" /> + <param name="blast_type" value="blastp" /> + <param name="out_format" value="5" /> + <param name="adv_opts_selector" value="advanced" /> + <param name="filter_query" value="False" /> + <param name="matrix" value="BLOSUM62" /> + <param name="max_hits" value="0" /> + <param name="word_size" value="0" /> + <param name="parse_deflines" value="True" /> + <output name="output1" file="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> + </test> + <test> + <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> + <param name="database" value="" /> + <param name="evalue_cutoff" value="1e-8" /> + <param name="blast_type" value="blastp" /> + <param name="out_format" value="6" /> + <param name="adv_opts_selector" value="advanced" /> + <param name="filter_query" value="False" /> + <param name="matrix" value="BLOSUM62" /> + <param name="max_hits" value="0" /> + <param name="word_size" value="0" /> + <param name="parse_deflines" value="True" /> + <output name="output1" file="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" /> + </test> + <test> + <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> + <param name="database" value="" /> + <param name="evalue_cutoff" value="1e-8" /> + <param name="blast_type" value="blastp" /> + <param name="out_format" value="ext" /> + <param name="adv_opts_selector" value="advanced" /> + <param name="filter_query" value="False" /> + <param name="matrix" value="BLOSUM62" /> + <param name="max_hits" value="0" /> + <param name="word_size" value="0" /> + <param name="parse_deflines" value="True" /> + <output name="output1" file="blastp_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" /> + </test> + <test> + <param name="query" value="rhodopsin_proteins.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="database" value="" /> + <param name="evalue_cutoff" value="1e-8" /> + <param name="blast_type" value="blastp" /> + <param name="out_format" value="6" /> + <param name="adv_opts_selector" value="basic" /> + <output name="output1" file="blastp_rhodopsin_vs_four_human.tabular" ftype="tabular" /> + </test> + </tests> + <help> + +.. class:: warningmark + +**Note**. Database searches may take a substantial amount of time. +For large input datasets it is advisable to allow overnight processing. + +----- + +**What it does** + +Search a *protein database* using a *protein query*, +using the NCBI BLAST+ blastp command line tool. + +----- + +**Output format** + +Because Galaxy focuses on processing tabular data, the default output of this +tool is tabular. The standard BLAST+ tabular output contains 12 columns: + +====== ========= ============================================ +Column NCBI name Description +------ --------- -------------------------------------------- + 1 qseqid Query Seq-id (ID of your sequence) + 2 sseqid Subject Seq-id (ID of the database hit) + 3 pident Percentage of identical matches + 4 length Alignment length + 5 mismatch Number of mismatches + 6 gapopen Number of gap openings + 7 qstart Start of alignment in query + 8 qend End of alignment in query + 9 sstart Start of alignment in subject (database hit) + 10 send End of alignment in subject (database hit) + 11 evalue Expectation value (E-value) + 12 bitscore Bit score +====== ========= ============================================ + +The BLAST+ tools can optionally output additional columns of information, +but this takes longer to calculate. Most (but not all) of these columns are +included by selecting the extended tabular output. The extra columns are +included *after* the standard 12 columns. This is so that you can write +workflow filtering steps that accept either the 12 or 24 column tabular +BLAST output. + +====== ============= =========================================== +Column NCBI name Description +------ ------------- ------------------------------------------- + 13 sallseqid All subject Seq-id(s), separated by a ';' + 14 score Raw score + 15 nident Number of identical matches + 16 positive Number of positive-scoring matches + 17 gaps Total number of gaps + 18 ppos Percentage of positive-scoring matches + 19 qframe Query frame + 20 sframe Subject frame + 21 qseq Aligned part of query sequence + 22 sseq Aligned part of subject sequence + 23 qlen Query sequence length + 24 slen Subject sequence length +====== ============= =========================================== + +The third option is BLAST XML output, which is designed to be parsed by +another program, and is understood by some Galaxy tools. + +You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). +The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. +The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. +The two query anchored outputs show a multiple sequence alignment between the query and all the matches, +and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). + +------- + +**References** + +Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. + +Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005. + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Thu Aug 23 09:00:40 2012 -0400 @@ -0,0 +1,264 @@ +<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.12"> + <description>Search protein database with translated nucleotide query sequence(s)</description> + <!-- If job splitting is enabled, break up the query file into parts --> + <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism> + <version_command>blastx -version</version_command> + <command interpreter="python">hide_stderr.py +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +blastx +-query "$query" +#if $db_opts.db_opts_selector == "db": + -db "${db_opts.database.fields.path}" +#else: + -subject "$db_opts.subject" +#end if +-query_gencode $query_gencode +-evalue $evalue_cutoff +-out $output1 +##Set the extended list here so if/when we add things, saved workflows are not affected +#if str($out_format)=="ext": + -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" +#else: + -outfmt $out_format +#end if +-num_threads 8 +#if $adv_opts.adv_opts_selector=="advanced": +$adv_opts.filter_query +$adv_opts.strand +-matrix $adv_opts.matrix +## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string +## Note -max_target_seqs overrides -num_descriptions and -num_alignments +#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): +-max_target_seqs $adv_opts.max_hits +#end if +#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): +-word_size $adv_opts.word_size +#end if +$adv_opts.ungapped +$adv_opts.parse_deflines +## End of advanced options: +#end if + </command> + <inputs> + <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="True">BLAST Database</option> + <option value="file">FASTA file (pairwise e-values)</option> + </param> + <when value="db"> + <param name="database" type="select" label="Protein BLAST database"> + <options from_file="blastdb_p.loc"> + <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="path" index="2"/> + </options> + </param> + <param name="subject" type="hidden" value="" /> + </when> + <when value="file"> + <param name="database" type="hidden" value="" /> + <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> + </when> + </conditional> + <param name="query_gencode" type="select" label="Query genetic code"> + <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> + <option value="1" select="True">1. Standard</option> + <option value="2">2. Vertebrate Mitochondrial</option> + <option value="3">3. Yeast Mitochondrial</option> + <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> + <option value="5">5. Invertebrate Mitochondrial</option> + <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> + <option value="9">9. Echinoderm Mitochondrial</option> + <option value="10">10. Euplotid Nuclear</option> + <option value="11">11. Bacteria and Archaea</option> + <option value="12">12. Alternative Yeast Nuclear</option> + <option value="13">13. Ascidian Mitochondrial</option> + <option value="14">14. Flatworm Mitochondrial</option> + <option value="15">15. Blepharisma Macronuclear</option> + <option value="16">16. Chlorophycean Mitochondrial Code</option> + <option value="21">21. Trematode Mitochondrial Code</option> + <option value="22">22. Scenedesmus obliquus mitochondrial Code</option> + <option value="23">23. Thraustochytrium Mitochondrial Code</option> + <option value="24">24. Pterobranchia mitochondrial code</option> + </param> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> + <param name="out_format" type="select" label="Output format"> + <option value="6" selected="True">Tabular (standard 12 columns)</option> + <option value="ext">Tabular (extended 24 columns)</option> + <option value="5">BLAST XML</option> + <option value="0">Pairwise text</option> + <option value="0 -html">Pairwise HTML</option> + <option value="2">Query-anchored text</option> + <option value="2 -html">Query-anchored HTML</option> + <option value="4">Flat query-anchored text</option> + <option value="4 -html">Flat query-anchored HTML</option> + <!-- + <option value="-outfmt 11">BLAST archive format (ASN.1)</option> + --> + </param> + <conditional name="adv_opts"> + <param name="adv_opts_selector" type="select" label="Advanced Options"> + <option value="basic" selected="True">Hide Advanced Options</option> + <option value="advanced">Show Advanced Options</option> + </param> + <when value="basic" /> + <when value="advanced"> + <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> + <param name="strand" type="select" label="Query strand(s) to search against database/subject"> + <option value="-strand both">Both</option> + <option value="-strand plus">Plus (forward)</option> + <option value="-strand minus">Minus (reverse complement)</option> + </param> + <param name="matrix" type="select" label="Scoring matrix"> + <option value="BLOSUM90">BLOSUM90</option> + <option value="BLOSUM80">BLOSUM80</option> + <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> + <option value="BLOSUM50">BLOSUM50</option> + <option value="BLOSUM45">BLOSUM45</option> + <option value="PAM250">PAM250</option> + <option value="PAM70">PAM70</option> + <option value="PAM30">PAM30</option> + </param> + <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> + <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param> + <!-- I'd like word_size to be optional, with minimum 2 for blastx --> + <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."> + <validator type="in_range" min="0" /> + </param> + <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> + <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/> + </when> + </conditional> + </inputs> + <outputs> + <data name="output1" format="tabular" label="blastx on ${db_opts.db_opts_selector}"> + <change_format> + <when input="out_format" value="0" format="txt"/> + <when input="out_format" value="0 -html" format="html"/> + <when input="out_format" value="2" format="txt"/> + <when input="out_format" value="2 -html" format="html"/> + <when input="out_format" value="4" format="txt"/> + <when input="out_format" value="4 -html" format="html"/> + <when input="out_format" value="5" format="blastxml"/> + </change_format> + </data> + </outputs> + <requirements> + <requirement type="binary">blastx</requirement> + </requirements> + <tests> + <test> + <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="database" value="" /> + <param name="evalue_cutoff" value="1e-10" /> + <param name="out_format" value="5" /> + <param name="adv_opts_selector" value="basic" /> + <output name="output1" file="blastx_rhodopsin_vs_four_human.xml" ftype="blastxml" /> + </test> + <test> + <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="database" value="" /> + <param name="evalue_cutoff" value="1e-10" /> + <param name="out_format" value="6" /> + <param name="adv_opts_selector" value="basic" /> + <output name="output1" file="blastx_rhodopsin_vs_four_human.tabular" ftype="tabular" /> + </test> + <test> + <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="database" value="" /> + <param name="evalue_cutoff" value="1e-10" /> + <param name="out_format" value="ext" /> + <param name="adv_opts_selector" value="basic" /> + <output name="output1" file="blastx_rhodopsin_vs_four_human_ext.tabular" ftype="tabular" /> + </test> + </tests> + <help> + +.. class:: warningmark + +**Note**. Database searches may take a substantial amount of time. +For large input datasets it is advisable to allow overnight processing. + +----- + +**What it does** + +Search a *protein database* using a *translated nucleotide query*, +using the NCBI BLAST+ blastx command line tool. + +----- + +**Output format** + +Because Galaxy focuses on processing tabular data, the default output of this +tool is tabular. The standard BLAST+ tabular output contains 12 columns: + +====== ========= ============================================ +Column NCBI name Description +------ --------- -------------------------------------------- + 1 qseqid Query Seq-id (ID of your sequence) + 2 sseqid Subject Seq-id (ID of the database hit) + 3 pident Percentage of identical matches + 4 length Alignment length + 5 mismatch Number of mismatches + 6 gapopen Number of gap openings + 7 qstart Start of alignment in query + 8 qend End of alignment in query + 9 sstart Start of alignment in subject (database hit) + 10 send End of alignment in subject (database hit) + 11 evalue Expectation value (E-value) + 12 bitscore Bit score +====== ========= ============================================ + +The BLAST+ tools can optionally output additional columns of information, +but this takes longer to calculate. Most (but not all) of these columns are +included by selecting the extended tabular output. The extra columns are +included *after* the standard 12 columns. This is so that you can write +workflow filtering steps that accept either the 12 or 24 column tabular +BLAST output. + +====== ============= =========================================== +Column NCBI name Description +------ ------------- ------------------------------------------- + 13 sallseqid All subject Seq-id(s), separated by a ';' + 14 score Raw score + 15 nident Number of identical matches + 16 positive Number of positive-scoring matches + 17 gaps Total number of gaps + 18 ppos Percentage of positive-scoring matches + 19 qframe Query frame + 20 sframe Subject frame + 21 qseq Aligned part of query sequence + 22 sseq Aligned part of subject sequence + 23 qlen Query sequence length + 24 slen Subject sequence length +====== ============= =========================================== + +The third option is BLAST XML output, which is designed to be parsed by +another program, and is understood by some Galaxy tools. + +You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). +The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. +The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. +The two query anchored outputs show a multiple sequence alignment between the query and all the matches, +and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). + +------- + +**References** + +Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Thu Aug 23 09:00:40 2012 -0400 @@ -0,0 +1,310 @@ +<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.12"> + <description>Search translated nucleotide database with protein query sequence(s)</description> + <!-- If job splitting is enabled, break up the query file into parts --> + <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism> + <version_command>tblastn -version</version_command> + <command interpreter="python">hide_stderr.py +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +tblastn +-query "$query" +#if $db_opts.db_opts_selector == "db": + -db "${db_opts.database.fields.path}" +#else: + -subject "$db_opts.subject" +#end if +-evalue $evalue_cutoff +-out $output1 +##Set the extended list here so if/when we add things, saved workflows are not affected +#if str($out_format)=="ext": + -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" +#else: + -outfmt $out_format +#end if +-num_threads 8 +#if $adv_opts.adv_opts_selector=="advanced": +-db_gencode $adv_opts.db_gencode +$adv_opts.filter_query +-matrix $adv_opts.matrix +## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string +## Note -max_target_seqs overrides -num_descriptions and -num_alignments +#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): +-max_target_seqs $adv_opts.max_hits +#end if +#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): +-word_size $adv_opts.word_size +#end if +##Ungapped disabled for now - see comments below +##$adv_opts.ungapped +$adv_opts.parse_deflines +## End of advanced options: +#end if + </command> + <inputs> + <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="True">BLAST Database</option> + <option value="file">FASTA file (pairwise e-values)</option> + </param> + <when value="db"> + <param name="database" type="select" label="Nucleotide BLAST database"> + <options from_file="blastdb.loc"> + <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="path" index="2"/> + </options> + </param> + <param name="subject" type="hidden" value="" /> + </when> + <when value="file"> + <param name="database" type="hidden" value="" /> + <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> + </when> + </conditional> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> + <param name="out_format" type="select" label="Output format"> + <option value="6" selected="True">Tabular (standard 12 columns)</option> + <option value="ext">Tabular (extended 24 columns)</option> + <option value="5">BLAST XML</option> + <option value="0">Pairwise text</option> + <option value="0 -html">Pairwise HTML</option> + <option value="2">Query-anchored text</option> + <option value="2 -html">Query-anchored HTML</option> + <option value="4">Flat query-anchored text</option> + <option value="4 -html">Flat query-anchored HTML</option> + <!-- + <option value="-outfmt 11">BLAST archive format (ASN.1)</option> + --> + </param> + <conditional name="adv_opts"> + <param name="adv_opts_selector" type="select" label="Advanced Options"> + <option value="basic" selected="True">Hide Advanced Options</option> + <option value="advanced">Show Advanced Options</option> + </param> + <when value="basic" /> + <when value="advanced"> + <param name="db_gencode" type="select" label="Database/subject genetic code"> + <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> + <option value="1" select="True">1. Standard</option> + <option value="2">2. Vertebrate Mitochondrial</option> + <option value="3">3. Yeast Mitochondrial</option> + <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> + <option value="5">5. Invertebrate Mitochondrial</option> + <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> + <option value="9">9. Echinoderm Mitochondrial</option> + <option value="10">10. Euplotid Nuclear</option> + <option value="11">11. Bacteria and Archaea</option> + <option value="12">12. Alternative Yeast Nuclear</option> + <option value="13">13. Ascidian Mitochondrial</option> + <option value="14">14. Flatworm Mitochondrial</option> + <option value="15">15. Blepharisma Macronuclear</option> + <option value="16">16. Chlorophycean Mitochondrial Code</option> + <option value="21">21. Trematode Mitochondrial Code</option> + <option value="22">22. Scenedesmus obliquus mitochondrial Code</option> + <option value="23">23. Thraustochytrium Mitochondrial Code</option> + <option value="24">24. Pterobranchia mitochondrial code</option> + </param> + <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> + <param name="matrix" type="select" label="Scoring matrix"> + <option value="BLOSUM90">BLOSUM90</option> + <option value="BLOSUM80">BLOSUM80</option> + <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> + <option value="BLOSUM50">BLOSUM50</option> + <option value="BLOSUM45">BLOSUM45</option> + <option value="PAM250">PAM250</option> + <option value="PAM70">PAM70</option> + <option value="PAM30">PAM30</option> + </param> + <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> + <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param> + <!-- I'd like word_size to be optional, with minimum 2 for blastp --> + <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."> + <validator type="in_range" min="0" /> + </param> + <!-- + Can't use '-ungapped' on its own, error back is: + Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search + Tried using '-ungapped -comp_based_stats F' and tblastn crashed with 'Attempt to access NULL pointer.' + <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" /> + --> + <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/> + </when> + </conditional> + </inputs> + <outputs> + <data name="output1" format="tabular" label="tblastn on ${db_opts.db_opts_selector}"> + <change_format> + <when input="out_format" value="0" format="txt"/> + <when input="out_format" value="0 -html" format="html"/> + <when input="out_format" value="2" format="txt"/> + <when input="out_format" value="2 -html" format="html"/> + <when input="out_format" value="4" format="txt"/> + <when input="out_format" value="4 -html" format="html"/> + <when input="out_format" value="5" format="blastxml"/> + </change_format> + </data> + </outputs> + <requirements> + <requirement type="binary">tblastn</requirement> + </requirements> + <tests> + <test> + <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> + <param name="database" value="" /> + <param name="evalue_cutoff" value="1e-10" /> + <param name="out_format" value="5" /> + <param name="adv_opts_selector" value="advanced" /> + <param name="filter_query" value="false" /> + <param name="matrix" value="BLOSUM80" /> + <param name="max_hits" value="0" /> + <param name="word_size" value="0" /> + <param name="parse_deflines" value="false" /> + <output name="output1" file="tblastn_four_human_vs_rhodopsin.xml" ftype="blastxml" /> + </test> + <test> + <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> + <param name="database" value="" /> + <param name="evalue_cutoff" value="1e-10" /> + <param name="out_format" value="ext" /> + <param name="adv_opts_selector" value="advanced" /> + <param name="filter_query" value="false" /> + <param name="matrix" value="BLOSUM80" /> + <param name="max_hits" value="0" /> + <param name="word_size" value="0" /> + <param name="parse_deflines" value="false" /> + <output name="output1" file="tblastn_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" /> + </test> + <test> + <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> + <param name="database" value="" /> + <param name="evalue_cutoff" value="1e-10" /> + <param name="out_format" value="6" /> + <param name="adv_opts_selector" value="advanced" /> + <param name="filter_query" value="false" /> + <param name="matrix" value="BLOSUM80" /> + <param name="max_hits" value="0" /> + <param name="word_size" value="0" /> + <param name="parse_deflines" value="false" /> + <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" /> + </test> + <test> + <!-- Same as above, but parse deflines - on BLAST 2.2.25+ makes no difference --> + <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> + <param name="database" value="" /> + <param name="evalue_cutoff" value="1e-10" /> + <param name="out_format" value="6" /> + <param name="adv_opts_selector" value="advanced" /> + <param name="filter_query" value="false" /> + <param name="matrix" value="BLOSUM80" /> + <param name="max_hits" value="0" /> + <param name="word_size" value="0" /> + <param name="parse_deflines" value="true" /> + <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" /> + </test> + <test> + <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> + <param name="db_opts_selector" value="file" /> + <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" /> + <param name="database" value="" /> + <param name="evalue_cutoff" value="1e-10" /> + <param name="out_format" value="0 -html" /> + <param name="adv_opts_selector" value="advanced" /> + <param name="filter_query" value="false" /> + <param name="matrix" value="BLOSUM80" /> + <param name="max_hits" value="0" /> + <param name="word_size" value="0" /> + <param name="parse_deflines" value="false" /> + <output name="output1" file="tblastn_four_human_vs_rhodopsin.html" ftype="html" /> + </test> + </tests> + <help> + +.. class:: warningmark + +**Note**. Database searches may take a substantial amount of time. +For large input datasets it is advisable to allow overnight processing. + +----- + +**What it does** + +Search a *translated nucleotide database* using a *protein query*, +using the NCBI BLAST+ tblastn command line tool. + +----- + +**Output format** + +Because Galaxy focuses on processing tabular data, the default output of this +tool is tabular. The standard BLAST+ tabular output contains 12 columns: + +====== ========= ============================================ +Column NCBI name Description +------ --------- -------------------------------------------- + 1 qseqid Query Seq-id (ID of your sequence) + 2 sseqid Subject Seq-id (ID of the database hit) + 3 pident Percentage of identical matches + 4 length Alignment length + 5 mismatch Number of mismatches + 6 gapopen Number of gap openings + 7 qstart Start of alignment in query + 8 qend End of alignment in query + 9 sstart Start of alignment in subject (database hit) + 10 send End of alignment in subject (database hit) + 11 evalue Expectation value (E-value) + 12 bitscore Bit score +====== ========= ============================================ + +The BLAST+ tools can optionally output additional columns of information, +but this takes longer to calculate. Most (but not all) of these columns are +included by selecting the extended tabular output. The extra columns are +included *after* the standard 12 columns. This is so that you can write +workflow filtering steps that accept either the 12 or 24 column tabular +BLAST output. + +====== ============= =========================================== +Column NCBI name Description +------ ------------- ------------------------------------------- + 13 sallseqid All subject Seq-id(s), separated by a ';' + 14 score Raw score + 15 nident Number of identical matches + 16 positive Number of positive-scoring matches + 17 gaps Total number of gaps + 18 ppos Percentage of positive-scoring matches + 19 qframe Query frame + 20 sframe Subject frame + 21 qseq Aligned part of query sequence + 22 sseq Aligned part of subject sequence + 23 qlen Query sequence length + 24 slen Subject sequence length +====== ============= =========================================== + +The third option is BLAST XML output, which is designed to be parsed by +another program, and is understood by some Galaxy tools. + +You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). +The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. +The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. +The two query anchored outputs show a multiple sequence alignment between the query and all the matches, +and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). + +------- + +**References** + +Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Thu Aug 23 09:00:40 2012 -0400 @@ -0,0 +1,252 @@ +<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.12"> + <description>Search translated nucleotide database with translated nucleotide query sequence(s)</description> + <!-- If job splitting is enabled, break up the query file into parts --> + <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism> + <version_command>tblastx -version</version_command> + <command interpreter="python">hide_stderr.py +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +tblastx +-query "$query" +#if $db_opts.db_opts_selector == "db": + -db "${db_opts.database.fields.path}" +#else: + -subject "$db_opts.subject" +#end if +-query_gencode $query_gencode +-evalue $evalue_cutoff +-out $output1 +##Set the extended list here so if/when we add things, saved workflows are not affected +#if str($out_format)=="ext": + -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" +#else: + -outfmt $out_format +#end if +-num_threads 8 +#if $adv_opts.adv_opts_selector=="advanced": +-db_gencode $adv_opts.db_gencode +$adv_opts.filter_query +$adv_opts.strand +-matrix $adv_opts.matrix +## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string +## Note -max_target_seqs overrides -num_descriptions and -num_alignments +#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): +-max_target_seqs $adv_opts.max_hits +#end if +#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): +-word_size $adv_opts.word_size +#end if +$adv_opts.parse_deflines +## End of advanced options: +#end if + </command> + <inputs> + <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="True">BLAST Database</option> + <option value="file">FASTA file (pairwise e-values)</option> + </param> + <when value="db"> + <param name="database" type="select" label="Nucleotide BLAST database"> + <options from_file="blastdb.loc"> + <column name="value" index="0"/> + <column name="name" index="1"/> + <column name="path" index="2"/> + </options> + </param> + <param name="subject" type="hidden" value="" /> + </when> + <when value="file"> + <param name="database" type="hidden" value="" /> + <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> + </when> + </conditional> + <param name="query_gencode" type="select" label="Query genetic code"> + <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> + <option value="1" select="True">1. Standard</option> + <option value="2">2. Vertebrate Mitochondrial</option> + <option value="3">3. Yeast Mitochondrial</option> + <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> + <option value="5">5. Invertebrate Mitochondrial</option> + <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> + <option value="9">9. Echinoderm Mitochondrial</option> + <option value="10">10. Euplotid Nuclear</option> + <option value="11">11. Bacteria and Archaea</option> + <option value="12">12. Alternative Yeast Nuclear</option> + <option value="13">13. Ascidian Mitochondrial</option> + <option value="14">14. Flatworm Mitochondrial</option> + <option value="15">15. Blepharisma Macronuclear</option> + <option value="16">16. Chlorophycean Mitochondrial Code</option> + <option value="21">21. Trematode Mitochondrial Code</option> + <option value="22">22. Scenedesmus obliquus mitochondrial Code</option> + <option value="23">23. Thraustochytrium Mitochondrial Code</option> + <option value="24">24. Pterobranchia mitochondrial code</option> + </param> + <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> + <param name="out_format" type="select" label="Output format"> + <option value="6" selected="True">Tabular (standard 12 columns)</option> + <option value="ext">Tabular (extended 24 columns)</option> + <option value="5">BLAST XML</option> + <option value="0">Pairwise text</option> + <option value="0 -html">Pairwise HTML</option> + <option value="2">Query-anchored text</option> + <option value="2 -html">Query-anchored HTML</option> + <option value="4">Flat query-anchored text</option> + <option value="4 -html">Flat query-anchored HTML</option> + <!-- + <option value="-outfmt 11">BLAST archive format (ASN.1)</option> + --> + </param> + <conditional name="adv_opts"> + <param name="adv_opts_selector" type="select" label="Advanced Options"> + <option value="basic" selected="True">Hide Advanced Options</option> + <option value="advanced">Show Advanced Options</option> + </param> + <when value="basic" /> + <when value="advanced"> + <param name="db_gencode" type="select" label="Database/subject genetic code"> + <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> + <option value="1" select="True">1. Standard</option> + <option value="2">2. Vertebrate Mitochondrial</option> + <option value="3">3. Yeast Mitochondrial</option> + <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> + <option value="5">5. Invertebrate Mitochondrial</option> + <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> + <option value="9">9. Echinoderm Mitochondrial</option> + <option value="10">10. Euplotid Nuclear</option> + <option value="11">11. Bacteria and Archaea</option> + <option value="12">12. Alternative Yeast Nuclear</option> + <option value="13">13. Ascidian Mitochondrial</option> + <option value="14">14. Flatworm Mitochondrial</option> + <option value="15">15. Blepharisma Macronuclear</option> + <option value="16">16. Chlorophycean Mitochondrial Code</option> + <option value="21">21. Trematode Mitochondrial Code</option> + <option value="22">22. Scenedesmus obliquus mitochondrial Code</option> + <option value="23">23. Thraustochytrium Mitochondrial Code</option> + <option value="24">24. Pterobranchia mitochondrial code</option> + </param> + <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> + <param name="strand" type="select" label="Query strand(s) to search against database/subject"> + <option value="-strand both">Both</option> + <option value="-strand plus">Plus (forward)</option> + <option value="-strand minus">Minus (reverse complement)</option> + </param> + <param name="matrix" type="select" label="Scoring matrix"> + <option value="BLOSUM90">BLOSUM90</option> + <option value="BLOSUM80">BLOSUM80</option> + <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> + <option value="BLOSUM50">BLOSUM50</option> + <option value="BLOSUM45">BLOSUM45</option> + <option value="PAM250">PAM250</option> + <option value="PAM70">PAM70</option> + <option value="PAM30">PAM30</option> + </param> + <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> + <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param> + <!-- I'd like word_size to be optional, with minimum 2 for tblastx --> + <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."> + <validator type="in_range" min="0" /> + </param> + <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/> + </when> + </conditional> + </inputs> + <outputs> + <data name="output1" format="tabular" label="tblastx on ${db_opts.db_opts_selector}"> + <change_format> + <when input="out_format" value="0" format="txt"/> + <when input="out_format" value="0 -html" format="html"/> + <when input="out_format" value="2" format="txt"/> + <when input="out_format" value="2 -html" format="html"/> + <when input="out_format" value="4" format="txt"/> + <when input="out_format" value="4 -html" format="html"/> + <when input="out_format" value="5" format="blastxml"/> + </change_format> + </data> + </outputs> + <requirements> + <requirement type="binary">tblastx</requirement> + </requirements> + <help> + +.. class:: warningmark + +**Note**. Database searches may take a substantial amount of time. +For large input datasets it is advisable to allow overnight processing. + +----- + +**What it does** + +Search a *translated nucleotide database* using a *protein query*, +using the NCBI BLAST+ tblastx command line tool. + +----- + +**Output format** + +Because Galaxy focuses on processing tabular data, the default output of this +tool is tabular. The standard BLAST+ tabular output contains 12 columns: + +====== ========= ============================================ +Column NCBI name Description +------ --------- -------------------------------------------- + 1 qseqid Query Seq-id (ID of your sequence) + 2 sseqid Subject Seq-id (ID of the database hit) + 3 pident Percentage of identical matches + 4 length Alignment length + 5 mismatch Number of mismatches + 6 gapopen Number of gap openings + 7 qstart Start of alignment in query + 8 qend End of alignment in query + 9 sstart Start of alignment in subject (database hit) + 10 send End of alignment in subject (database hit) + 11 evalue Expectation value (E-value) + 12 bitscore Bit score +====== ========= ============================================ + +The BLAST+ tools can optionally output additional columns of information, +but this takes longer to calculate. Most (but not all) of these columns are +included by selecting the extended tabular output. The extra columns are +included *after* the standard 12 columns. This is so that you can write +workflow filtering steps that accept either the 12 or 24 column tabular +BLAST output. + +====== ============= =========================================== +Column NCBI name Description +------ ------------- ------------------------------------------- + 13 sallseqid All subject Seq-id(s), separated by a ';' + 14 score Raw score + 15 nident Number of identical matches + 16 positive Number of positive-scoring matches + 17 gaps Total number of gaps + 18 ppos Percentage of positive-scoring matches + 19 qframe Query frame + 20 sframe Subject frame + 21 qseq Aligned part of query sequence + 22 sseq Aligned part of subject sequence + 23 qlen Query sequence length + 24 slen Subject sequence length +====== ============= =========================================== + +The third option is BLAST XML output, which is designed to be parsed by +another program, and is understood by some Galaxy tools. + +You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). +The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. +The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. +The two query anchored outputs show a multiple sequence alignment between the query and all the matches, +and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). + +------- + +**References** + +Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/tool_dependencies.xml Thu Aug 23 09:00:40 2012 -0400 @@ -0,0 +1,21 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="blast+" version="2.2.26+"> + <install version="1.0"> + <actions> + <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-src.tar.gz</action> + <action type="shell_command">cd c++ && ./configure --prefix=$INSTALL_DIR && make && make install</action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +These links provide information for building the NCBI Blast+ package in most environments. + +System requirements +http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download + </readme> + </package> +</tool_dependency> +