# HG changeset patch
# User peterjc
# Date 1366206265 14400
# Node ID c848371164578aa878e6a3af060e6748da25ceb3
# Parent b04f55ab182cef66b744898f159798b3e247a50a
Uploaded v0.0.14
diff -r b04f55ab182c -r c84837116457 tools/ncbi_blast_plus/hide_stderr.py
--- a/tools/ncbi_blast_plus/hide_stderr.py Wed Apr 17 09:44:04 2013 -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)
diff -r b04f55ab182c -r c84837116457 tools/ncbi_blast_plus/ncbi_blast_plus.txt
--- a/tools/ncbi_blast_plus/ncbi_blast_plus.txt Wed Apr 17 09:44:04 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blast_plus.txt Wed Apr 17 09:44:25 2013 -0400
@@ -8,9 +8,10 @@
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
+Note that these wrappers (and the associated datetypes) were originally
+distributed as part of the main Galaxy repository, but as of August 2012
+moved to the Galaxy Tool Shed as 'ncbi_blast_plus' (and 'blast_datatypes').
+My thanks to Dannon Baker from the Galaxy development team for his assistance
with this.
@@ -25,7 +26,7 @@
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
+You will also need to install 'blast_datatypes' from the Tool Shed. This
defines the BLAST XML file format ('blastxml').
@@ -39,6 +40,10 @@
very large sets of queries where BLAST+ can become memory hungry)
- Include warning that BLAST+ with subject FASTA gives pairwise
e-values
+v0.0.13 - Use the new error handling options in Galaxy (the previously
+ bundled hide_stderr.py script is no longer needed).
+v0.0.14 - Support for makeblastdb and local BLAST databases in the history
+ (using work from Edward Kirton).
Developers
diff -r b04f55ab182c -r c84837116457 tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Wed Apr 17 09:44:25 2013 -0400
@@ -0,0 +1,63 @@
+
+ Show BLAST database information from blastdbcmd
+
+blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" -info -out $info
+
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+ blastdbcmd
+
+
+
+**What it does**
+
+Calls the NCBI BLAST+ blastdbcmd command line tool with the -info
+switch to give summary information about a BLAST database, such as
+the size (number of sequences and total length) and date.
+
+-------
+
+**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.
+
+
+
diff -r b04f55ab182c -r c84837116457 tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Wed Apr 17 09:44:25 2013 -0400
@@ -0,0 +1,135 @@
+
+ Extract sequence(s) from BLAST database
+
+## The command is a Cheetah template which allows some Python based syntax.
+## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
+blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}"
+
+##TODO: What about -ctrl_a and -target_only as advanced options?
+
+#if $id_opts.id_type=="file":
+-entry_batch "$id_opts.entries"
+#else:
+##Perform some simple search/replaces to remove whitespace
+##and make it comma separated, and escape any pipe characters
+-entry "$id_opts.entries.replace('\r',',').replace('\n',',').replace(' ','').replace(',,',',').replace(',,',',').strip(',').replace('|','\|')"
+#end if
+
+##When building a BLAST database, to ensure unique IDs makeblastdb will
+##do things like turning a FASTA entry with ID of ERP44 into lcl|ERP44
+##(if using -parse_seqids) or simply assign it an ID using the record
+##number like gnl|BL_ORD_ID|123 (to cope with duplicate IDs in the FASTA
+##file). In -parse_seqids mode, a duplicate FASTA ID gives an error.
+##
+##The BLAST plain text and XML output will contain these BLAST IDs, but
+##the tabular output does not (at least, not in BLAST 2.2.25+).
+##Therefore in general, Galaxy users won't care about the (internal)
+##BLAST identifiers.
+##
+##The blastdbcmd FASTA output will also contain these IDs, but in the
+##context of the BLAST tabular output they are not helpful. Therefore
+##to recover the original ID as used in the FASTA file for makeblastdb
+##we need a litte post processing.
+##
+##We remove the NCBI's lcl|... or gnl|BL_ORD_ID|123 prefixes
+##using sed, however the exact syntax differs for Mac OS X's sed
+
+#if str($outfmt)=="blastid":
+-out "$seq"
+#else if sys.platform == "darwin":
+| sed -E 's/^>(lcl\||gnl\|BL_ORD_ID\|[0-9]* )/>/1' > "$seq"
+#else:
+| sed 's/>\(lcl|\|gnl|BL_ORD_ID|[0-9]* \)/>/1' > "$seq"
+#end if
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+ blastdbcmd
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+**What it does**
+
+Extracts FASTA formatted sequences from a BLAST database
+using the NCBI BLAST+ blastdbcmd command line tool.
+
+.. class:: warningmark
+
+**BLAST assigned identifiers**
+
+When a BLAST database is constructed from a FASTA file, the
+original identifiers can be replaced with BLAST assigned
+identifiers, partly to ensure uniqueness. e.g. Sometimes
+a prefix of 'lcl|' is added (lcl is short for local),
+or an arbitrary name starting 'gnl|BL_ORD_ID|' is created.
+
+If you are using the tabular output from BLAST, it will contain
+the original identifiers - not the BLAST assigned identifiers
+suitable for use with the blastdbcmd tool.
+
+If you are using the XML or plain text output, this will also
+contain the BLAST assigned identifiers. However, this means
+getting a list of BLAST assigned identifiers isn't straightforward.
+
+-------
+
+**References**
+
+Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
+
+Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005.
+
+
+
diff -r b04f55ab182c -r c84837116457 tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Wed Apr 17 09:44:04 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Wed Apr 17 09:44:25 2013 -0400
@@ -1,15 +1,17 @@
-
+Search nucleotide database with nucleotide query sequence(s)
-
+ blastn -version
- hide_stderr.py
+
## The command is a Cheetah template which allows some Python based syntax.
## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
blastn
-query "$query"
#if $db_opts.db_opts_selector == "db":
-db "${db_opts.database.fields.path}"
+#elif $db_opts.db_opts_selector == "histdb":
+ -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}"
#else:
-subject "$db_opts.subject"
#end if
@@ -39,12 +41,21 @@
## End of advanced options:
#end if
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@@ -54,10 +65,17 @@
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diff -r b04f55ab182c -r c84837116457 tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Wed Apr 17 09:44:04 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Wed Apr 17 09:44:25 2013 -0400
@@ -1,15 +1,17 @@
-
+Search protein database with protein query sequence(s)
-
+ blastp -version
- 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}"
+#elif $db_opts.db_opts_selector == "histdb":
+ -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}"
#else:
-subject "$db_opts.subject"
#end if
@@ -40,12 +42,21 @@
## End of advanced options:
#end if
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diff -r b04f55ab182c -r c84837116457 tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Wed Apr 17 09:44:04 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Wed Apr 17 09:44:25 2013 -0400
@@ -1,15 +1,17 @@
-
+Search protein database with translated nucleotide query sequence(s)
-
+ blastx -version
- 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}"
+#elif $db_opts.db_opts_selector == "histdb":
+ -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}"
#else:
-subject "$db_opts.subject"
#end if
@@ -40,12 +42,21 @@
## End of advanced options:
#end if
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@@ -55,10 +66,17 @@
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diff -r b04f55ab182c -r c84837116457 tools/ncbi_blast_plus/ncbi_makeblastdb.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Wed Apr 17 09:44:25 2013 -0400
@@ -0,0 +1,121 @@
+
+Make BLAST database
+makeblastdb -version
+
+makeblastdb -out ${os.path.join($outfile.extra_files_path,'blastdb')}
+$parse_seqids
+$hash_index
+## Single call to -in with multiple filenames space separated with outer quotes
+## (presumably any filenames with spaces would be a problem). Note this gives
+## some extra spaces, e.g. -in " file1 file2 file3 " but BLAST seems happy:
+-in "
+#for $i in $in
+${i.file} #end for
+"
+#if $title:
+-title "$title"
+#else:
+##Would default to being based on the cryptic Galaxy filenames, which is unhelpful
+-title "BLAST Database"
+#end if
+-dbtype $dbtype
+## #set $sep = '-mask_data '
+## #for $i in $mask_data
+## $sep${i.file}
+## #set $set = ', '
+## #end for
+## #set $sep = '-gi_mask -gi_mask_name '
+## #for $i in $gi_mask
+## $sep${i.file}
+## #set $set = ', '
+## #end for
+## #if $tax.select == 'id':
+## -taxid $tax.id
+## #else if $tax.select == 'map':
+## -taxid_map $tax.map
+## #end if
+
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+ makeblastdb
+
+
+**What it does**
+
+Make BLAST database from one or more FASTA files and/or BLAST databases.
+
+This is a wrapper for the NCBI BLAST+ tool 'makeblastdb', which is the
+replacement for the 'formatdb' tool in the NCBI 'legacy' BLAST suite.
+
+
+
+**Documentation**
+
+http://www.ncbi.nlm.nih.gov/books/NBK1763/
+
+
diff -r b04f55ab182c -r c84837116457 tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Wed Apr 17 09:44:04 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Wed Apr 17 09:44:25 2013 -0400
@@ -1,15 +1,17 @@
-
+Search translated nucleotide database with protein query sequence(s)
-
+ tblastn -version
- hide_stderr.py
+
## The command is a Cheetah template which allows some Python based syntax.
## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
tblastn
-query "$query"
#if $db_opts.db_opts_selector == "db":
-db "${db_opts.database.fields.path}"
+#elif $db_opts.db_opts_selector == "histdb":
+ -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}"
#else:
-subject "$db_opts.subject"
#end if
@@ -40,12 +42,21 @@
## End of advanced options:
#end if
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diff -r b04f55ab182c -r c84837116457 tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Wed Apr 17 09:44:04 2013 -0400
+++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Wed Apr 17 09:44:25 2013 -0400
@@ -1,15 +1,17 @@
-
+Search translated nucleotide database with translated nucleotide query sequence(s)
-
+ tblastx -version
- 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}"
+#elif $db_opts.db_opts_selector == "histdb":
+ -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}"
#else:
-subject "$db_opts.subject"
#end if
@@ -40,12 +42,21 @@
## End of advanced options:
#end if
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