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Main is at rev 1474:cea8c4d68ad0
by Greg Von Kuster 21 Aug '08

21 Aug '08

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[hg] galaxy 1474: Reverting extract_genomic_dna and blat_wrapper...
by greg＠scofield.bx.psu.edu 21 Aug '08

21 Aug '08

details: http://www.bx.psu.edu/hg/galaxy/rev/cea8c4d68ad0 changeset: 1474:cea8c4d68ad0 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Aug 21 08:54:51 2008 -0400 description: Reverting extract_genomic_dna and blat_wrapper tools to rev 1472. 2 file(s) affected in this change: tools/extract/extract_genomic_dna.py tools/metag_tools/blat_wrapper.py diffs (42 lines): diff -r 8cda62b46162 -r cea8c4d68ad0 tools/extract/extract_genomic_dna.py --- a/tools/extract/extract_genomic_dna.py Tue Aug 19 13:35:44 2008 -0400 +++ b/tools/extract/extract_genomic_dna.py Thu Aug 21 08:54:51 2008 -0400 @@ -35,7 +35,7 @@ for line in open( nib_file ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ) and line.startswith( 'seq' ): - fields = line.split() + fields = line.split( '\t' ) if len( fields ) < 3: continue if fields[1] == dbkey: @@ -49,7 +49,7 @@ for line in open( twobit_file ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ): - fields = line.split() + fields = line.split( '\t' ) if len( fields ) < 2: continue if fields[0] == dbkey: diff -r 8cda62b46162 -r cea8c4d68ad0 tools/metag_tools/blat_wrapper.py --- a/tools/metag_tools/blat_wrapper.py Tue Aug 19 13:35:44 2008 -0400 +++ b/tools/metag_tools/blat_wrapper.py Thu Aug 21 08:54:51 2008 -0400 @@ -15,7 +15,7 @@ for i, line in enumerate( file( nib_file ) ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ): - fields = line.split() + fields = line.split( '\t' ) if len( fields ) < 3: continue if fields[0] == 'seq': @@ -31,7 +31,7 @@ for i, line in enumerate( file( twobit_file ) ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ): - fields = line.split() + fields = line.split( '\t' ) if len( fields ) < 2: continue twobits[( fields[0] )] = fields[1]

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[hg] galaxy 1473: Unbreaking 2 tools that I just broke.
by greg＠scofield.bx.psu.edu 19 Aug '08

19 Aug '08

details: http://www.bx.psu.edu/hg/galaxy/rev/8cda62b46162 changeset: 1473:8cda62b46162 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Aug 19 13:35:44 2008 -0400 description: Unbreaking 2 tools that I just broke. 2 file(s) affected in this change: tools/extract/extract_genomic_dna.py tools/metag_tools/blat_wrapper.py diffs (42 lines): diff -r c81fa25c67e5 -r 8cda62b46162 tools/extract/extract_genomic_dna.py --- a/tools/extract/extract_genomic_dna.py Tue Aug 19 10:44:08 2008 -0400 +++ b/tools/extract/extract_genomic_dna.py Tue Aug 19 13:35:44 2008 -0400 @@ -35,7 +35,7 @@ for line in open( nib_file ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ) and line.startswith( 'seq' ): - fields = line.split( '\t' ) + fields = line.split() if len( fields ) < 3: continue if fields[1] == dbkey: @@ -49,7 +49,7 @@ for line in open( twobit_file ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ): - fields = line.split( '\t' ) + fields = line.split() if len( fields ) < 2: continue if fields[0] == dbkey: diff -r c81fa25c67e5 -r 8cda62b46162 tools/metag_tools/blat_wrapper.py --- a/tools/metag_tools/blat_wrapper.py Tue Aug 19 10:44:08 2008 -0400 +++ b/tools/metag_tools/blat_wrapper.py Tue Aug 19 13:35:44 2008 -0400 @@ -15,7 +15,7 @@ for i, line in enumerate( file( nib_file ) ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ): - fields = line.split( '\t' ) + fields = line.split() if len( fields ) < 3: continue if fields[0] == 'seq': @@ -31,7 +31,7 @@ for i, line in enumerate( file( twobit_file ) ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ): - fields = line.split( '\t' ) + fields = line.split() if len( fields ) < 2: continue twobits[( fields[0] )] = fields[1]

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Main is at rev 1472:c81fa25c67e5
by Greg Von Kuster 19 Aug '08

19 Aug '08

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[hg] galaxy 1472: Some tool fixes:
by Nate Coraor 19 Aug '08

19 Aug '08

details: http://www.bx.psu.edu/hg/galaxy/rev/c81fa25c67e5 changeset: 1472:c81fa25c67e5 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Aug 19 10:44:08 2008 -0400 description: Some tool fixes: 1) fix for interval_maf_to_merged_fasta when strand column not included in input metadata 2) Tools using alignseq.loc now split on TAB rather than wihite space 3 file(s) affected in this change: tools/extract/extract_genomic_dna.py tools/maf/interval_maf_to_merged_fasta.py tools/metag_tools/blat_wrapper.py diffs (84 lines): diff -r 1958657d8f8d -r c81fa25c67e5 tools/extract/extract_genomic_dna.py --- a/tools/extract/extract_genomic_dna.py Tue Aug 12 10:04:28 2008 -0400 +++ b/tools/extract/extract_genomic_dna.py Tue Aug 19 10:44:08 2008 -0400 @@ -35,7 +35,7 @@ for line in open( nib_file ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ) and line.startswith( 'seq' ): - fields = line.split() + fields = line.split( '\t' ) if len( fields ) < 3: continue if fields[1] == dbkey: @@ -49,7 +49,7 @@ for line in open( twobit_file ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ): - fields = line.split() + fields = line.split( '\t' ) if len( fields ) < 2: continue if fields[0] == dbkey: diff -r 1958657d8f8d -r c81fa25c67e5 tools/maf/interval_maf_to_merged_fasta.py --- a/tools/maf/interval_maf_to_merged_fasta.py Tue Aug 12 10:04:28 2008 -0400 +++ b/tools/maf/interval_maf_to_merged_fasta.py Tue Aug 19 10:44:08 2008 -0400 @@ -67,25 +67,29 @@ sys.exit() if not options.geneBED: - if options.chromCol: chr_col = int( options.chromCol ) - 1 + if options.chromCol: + chr_col = int( options.chromCol ) - 1 else: - print >>sys.stderr, "Chromosome column has not been specified." + print >>sys.stderr, "Chromosome column not set, click the pencil icon in the history item to set the metadata attributes." sys.exit() - if options.startCol: start_col = int( options.startCol ) - 1 + if options.startCol: + start_col = int( options.startCol ) - 1 else: - print >>sys.stderr, "Start column has not been specified." + print >>sys.stderr, "Start column not set, click the pencil icon in the history item to set the metadata attributes." sys.exit() - if options.endCol: end_col = int( options.endCol ) - 1 + if options.endCol: + end_col = int( options.endCol ) - 1 else: - print >>sys.stderr, "End column has not been specified." + print >>sys.stderr, "End column not set, click the pencil icon in the history item to set the metadata attributes." sys.exit() - if options.strandCol: strand_col = int( options.strandCol ) - 1 + if options.strandCol: + strand_col = int( options.strandCol ) - 1 else: - print >>sys.stderr, "Strand column has not been specified." - sys.exit() + strandCol = -1 + mafIndexFile = "%s/maf_index.loc" % options.mafIndexFileDir #Finish parsing command line diff -r 1958657d8f8d -r c81fa25c67e5 tools/metag_tools/blat_wrapper.py --- a/tools/metag_tools/blat_wrapper.py Tue Aug 12 10:04:28 2008 -0400 +++ b/tools/metag_tools/blat_wrapper.py Tue Aug 19 10:44:08 2008 -0400 @@ -15,7 +15,7 @@ for i, line in enumerate( file( nib_file ) ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ): - fields = line.split() + fields = line.split( '\t' ) if len( fields ) < 3: continue if fields[0] == 'seq': @@ -31,7 +31,7 @@ for i, line in enumerate( file( twobit_file ) ): line = line.rstrip( '\r\n' ) if line and not line.startswith( "#" ): - fields = line.split() + fields = line.split( '\t' ) if len( fields ) < 2: continue twobits[( fields[0] )] = fields[1]

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New (reckless) tools
by Assaf Gordon 18 Aug '08

18 Aug '08

Hello, I'd like to share three tools that I've recently made. One is semi-useful, the other too are completely reckless. The first one is an improved "sort" tool, which allows sorting according to multiple keys. it uses the GNU sort utility, and therefor doesn't need a script file (except for the XML itself). BEGIN SORT TOOL --------------- <tool id="cshl_sort_tool" name="Sort"> <command>sort #for $key in $sortkeys '-k ${key.column},${key.column}${key.order}${key.style}' #end for $input > $out_file1</command> <inputs> <param format="txt" name="input" type="data" label="Sort Query" /> <repeat name="sortkeys" title="sort key"> <param name="column" label="on column" type="data_column" data_ref="input" accept_default="true" /> <param name="order" type="select" display="radio" label="in"> <option value="r">Descending order</option> <option value="">Ascending order</option> </param> <param name="style" type="select" display="radio" label="Flavor"> <option value="n">Numerical sort</option> <option value="">Alphabetical sort</option> </param> </repeat> </inputs> <outputs> <data format="input" name="out_file1" metadata_source="input"/> </outputs> </tool> -------------- END SORT TOOL The two other tools allow running AWK and SED directly from galaxy. These should NEVER EVER be installed on a publicly accessible system (as a matter of fact, these shouldn't be install on any system... ) The reason I wrote these tools, is that sometimes the galaxy tools just can't do something which would be very simple to do, if I just had access to sed or awk. This usually happens when biologists here work on galaxy, and get 'stuck' trying to do something which just can't be done with the current galaxy tools. Then they ask me to do it. One way (for me) to do it is to SSH into the galaxy server, get the dataset file, run sed/awk, create a new file, and manually upload it back to galaxy. Another way is to run awk and sed from within galaxy... I won't say this is the most elegant solution ever - but it gets the job done. Note about security: With these tools - there is NONE. An AWK script can execute shell commands (the 'system' function) and can read any local file (the 'getline' command). A SED script can read files (the 'r' command) and write files (the 'w' command). The 'password' field is completely useless. The password is not hidden, and the web browser will probably cache it and display it the next time you access the tool's page. BEGIN AWK TOOL -------------- <tool id="cshl_awk_tool" name="awk"> <command>awk '$url_paste' OFS="\t" $input > $output </command> <inputs> <param format="txt" name="input" type="data" label="File to process" />  <param name="url_paste" type="text" area="true" size="5x35" label="AWK Program" help=""> <validator type="expression" message="Invalid Program!">value.find('\'')==-1</validator> </param>  <param name="passwd" type="text" area="false" label="Secret password"> <validator type="regex" message="Oops! wrong password.">^awk$</validator> </param> </inputs> <outputs> <data format="txt" name="output" metadata_source="input" /> </outputs> </tool> -------------- END AWK TOOL BEGIN SED TOOL -------------- <tool id="cshl_sed_tool" name="sed"> <command>sed '$url_paste' $input > $output </command> <inputs> <param format="txt" name="input" type="data" label="File to process" />  <param name="url_paste" type="text" area="true" size="5x35" label="SED Program" help=""> <validator type="expression" message="Invalid Program!">value.find('\'')==-1</validator> </param>  <param name="passwd" type="text" area="false" label="Secret password"> <validator type="regex" message="Oops! wrong password.">^sed$</validator> </param> </inputs> <outputs> <data format="txt" name="output" metadata_source="input" /> </outputs> </tool> -------------- END SED TOOL The above XML snippets are free for use under the same license as galaxy (the LICENSE.txt file). -Gordon.

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Main is at rev 1471:1958657d8f8d
by Greg Von Kuster 12 Aug '08

12 Aug '08

1 0

[hg] galaxy 1471: Fix for interval2maf.py when metadata missing ...
by greg＠scofield.bx.psu.edu 12 Aug '08

12 Aug '08

details: http://www.bx.psu.edu/hg/galaxy/rev/1958657d8f8d changeset: 1471:1958657d8f8d user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Aug 12 10:04:28 2008 -0400 description: Fix for interval2maf.py when metadata missing strand column value. 1 file(s) affected in this change: tools/maf/interval2maf.py diffs (31 lines): diff -r 78e84936b7a3 -r 1958657d8f8d tools/maf/interval2maf.py --- a/tools/maf/interval2maf.py Tue Aug 12 09:18:47 2008 -0400 +++ b/tools/maf/interval2maf.py Tue Aug 12 10:04:28 2008 -0400 @@ -54,23 +54,22 @@ if options.chromCol: chromCol = int( options.chromCol ) - 1 else: - print >>sys.stderr, "Chromosome column has not been specified." + print >>sys.stderr, "Chromosome column not set, click the pencil icon in the history item to set the metadata attributes." sys.exit() if options.startCol: startCol = int( options.startCol ) - 1 else: - print >>sys.stderr, "Start column has not been specified." + print >>sys.stderr, "Start column not set, click the pencil icon in the history item to set the metadata attributes." sys.exit() if options.endCol: endCol = int( options.endCol ) - 1 else: - print >>sys.stderr, "End column has not been specified." + print >>sys.stderr, "End column not set, click the pencil icon in the history item to set the metadata attributes." sys.exit() if options.strandCol: strandCol = int( options.strandCol ) - 1 else: - print >>sys.stderr, "Strand column has not been specified." - sys.exit() + strandCol = -1 if options.interval_file: interval_file = options.interval_file else:

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Main is at rev 1470:78e84936b7a3
by Nate Coraor 12 Aug '08

12 Aug '08

1 0

[hg] galaxy 1470: Fix for Extract Genomic DNA when input file me...
by Nate Coraor 12 Aug '08

12 Aug '08

details: http://www.bx.psu.edu/hg/galaxy/rev/78e84936b7a3 changeset: 1470:78e84936b7a3 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Aug 12 09:18:47 2008 -0400 description: Fix for Extract Genomic DNA when input file metadata missing strand column value. 2 file(s) affected in this change: tools/extract/extract_genomic_dna.py tools/extract/extract_genomic_dna.xml diffs (79 lines): diff -r b9142bbae4ad -r 78e84936b7a3 tools/extract/extract_genomic_dna.py --- a/tools/extract/extract_genomic_dna.py Fri Aug 08 13:42:32 2008 -0400 +++ b/tools/extract/extract_genomic_dna.py Tue Aug 12 09:18:47 2008 -0400 @@ -1,7 +1,10 @@ #!/usr/bin/env python """ -usage: extract_genomic_dna.py $input $out_file1 ${input.metadata.chromCol} ${input.metadata.startCol} ${input.metadata.endCol} ${input.metadata.strandCol} $dbkey $out_format GALAXY_DATA_INDEX_DIR -by Wen-Yu Chung +usage: %prog $input $out_file1 + -1, --cols=N,N,N,N: Columns for start, end, strand in input file + -d, --dbkey=N: Genome build of input file + -o, --output_format=N: the data type of the output file + -g, --GALAXY_DATA_INDEX_DIR=N: the directory containing alignseq.loc and twobit.loc """ from galaxy import eggs import pkg_resources @@ -10,6 +13,7 @@ from bx.cookbook import doc_optparse import bx.seq.nib import bx.seq.twobit +from galaxy.tools.util.galaxyops import * assert sys.version_info[:2] >= ( 2, 4 ) @@ -54,32 +58,18 @@ return twobit_path def __main__(): - input_filename = sys.argv[1] - output_filename = sys.argv[2] - includes_strand_col = False + options, args = doc_optparse.parse( __doc__ ) + try: + chrom_col, start_col, end_col, strand_col = parse_cols_arg( options.cols ) + dbkey = options.dbkey + output_format = options.output_format + GALAXY_DATA_INDEX_DIR = options.GALAXY_DATA_INDEX_DIR + input_filename, output_filename = args + except: + doc_optparse.exception() + + includes_strand_col = strand_col >= 0 strand = None - # If any of the following exceptions are thrown, we need to improve the metadata validator. - try: - chrom_col = int( sys.argv[3] ) - 1 - except: - stop_err( "Chrom column not properly set, click the pencil icon in your history item to set it." ) - try: - start_col = int( sys.argv[4] ) - 1 - except: - stop_err( "Start column not properly set, click the pencil icon in your history item to set it." ) - try: - end_col = int( sys.argv[5] ) - 1 - except: - stop_err( "End column not properly set, click the pencil icon in your history item to set it." ) - try: - strand_col = int( sys.argv[6] ) - 1 - if strand_col >= 0: - includes_strand_col = True - except: - pass - dbkey = sys.argv[7] - output_format = sys.argv[8] - GALAXY_DATA_INDEX_DIR = sys.argv[9] nibs = {} twobits = {} nib_path = check_nib_file( dbkey, GALAXY_DATA_INDEX_DIR ) diff -r b9142bbae4ad -r 78e84936b7a3 tools/extract/extract_genomic_dna.xml --- a/tools/extract/extract_genomic_dna.xml Fri Aug 08 13:42:32 2008 -0400 +++ b/tools/extract/extract_genomic_dna.xml Tue Aug 12 09:18:47 2008 -0400 @@ -1,6 +1,6 @@ <tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.1.0"> <description>using coordinates from assembled/unassembled genomes</description> - <command interpreter="python">extract_genomic_dna.py $input $out_file1 ${input.metadata.chromCol} ${input.metadata.startCol} ${input.metadata.endCol} ${input.metadata.strandCol} $dbkey $out_format ${GALAXY_DATA_INDEX_DIR}</command> + <command interpreter="python">extract_genomic_dna.py $input $out_file1 -1 ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol} -d $dbkey -o $out_format -g ${GALAXY_DATA_INDEX_DIR}</command> <inputs> <param format="interval" name="input" type="data" label="Fetch sequences corresponding to Query"> <validator type="unspecified_build" />

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