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commit/galaxy-central: dan: Allow importing one's own history.
by Bitbucket 22 Mar '11

22 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/dc9efb540f61/ changeset: r5248:dc9efb540f61 user: dan date: 2011-03-23 00:43:32 summary: Allow importing one's own history. affected #: 1 file (49 bytes) --- a/lib/galaxy/web/controllers/history.py Tue Mar 22 17:49:09 2011 -0400 +++ b/lib/galaxy/web/controllers/history.py Tue Mar 22 19:43:32 2011 -0400 @@ -669,8 +669,9 @@ if not trans.user_is_admin() and not self.security_check( user, import_history, check_ownership=False, check_accessible=True ): return trans.show_error_message( "You cannot access this history.<br>You can %s." % referer_message, use_panels=True ) if user: - if import_history.user_id == user.id: - return trans.show_error_message( "You cannot import your own history.<br>You can %s." % referer_message, use_panels=True ) + #dan: I can import my own history. + #if import_history.user_id == user.id: + # return trans.show_error_message( "You cannot import your own history.<br>You can %s." % referer_message, use_panels=True ) new_history = import_history.copy( target_user=user ) new_history.name = "imported: " + new_history.name new_history.user_id = user.id Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: kanwei: Refactor Grouping tool and fix bug where data after a blank value in the group_by column returns the wrong data.
by Bitbucket 22 Mar '11

22 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4d521da04318/ changeset: r5247:4d521da04318 user: kanwei date: 2011-03-22 22:49:09 summary: Refactor Grouping tool and fix bug where data after a blank value in the group_by column returns the wrong data. affected #: 2 files (5.1 KB) --- a/tools/stats/grouping.py Tue Mar 22 14:08:32 2011 -0400 +++ b/tools/stats/grouping.py Tue Mar 22 17:49:09 2011 -0400 @@ -1,10 +1,12 @@ #!/usr/bin/env python -#Guruprasad Ananda +# Guruprasad Ananda +# Refactored 2011, Kanwei Li """ This tool provides the SQL "group by" functionality. """ import sys, string, re, commands, tempfile, random from rpy import * +from itertools import groupby def stop_err(msg): sys.stderr.write(msg) @@ -53,10 +55,10 @@ stop_err( "Group column not specified." ) str_ops = ['c', 'length', 'unique', 'random', 'cuniq', 'Mode'] #ops that can handle string/non-numeric inputs - for k,col in enumerate(cols): + for k, col in enumerate(cols): col = int(col)-1 if ops[k] not in str_ops: - # We'll get here only if the user didn't choose 'Concatenate' or 'Count' or 'Count Distinct' or 'pick randmly', which are the + # We'll get here only if the user didn't choose 'Concatenate' or 'Count' or 'Count Distinct' or 'pick randomly', which are the # only aggregation functions that can be used on columns containing strings. try: float( elems[col] ) @@ -90,191 +92,94 @@ if error_code != 0: stop_err( "Sorting input dataset resulted in error: %s: %s" %( error_code, stdout )) - prev_item = "" - prev_vals = [] + prev_item = None skipped_lines = 0 - first_invalid_line = 0 - invalid_line = '' + first_invalid_line = None invalid_value = '' invalid_column = 0 fout = open(sys.argv[1], "w") - for ii, line in enumerate( file( tmpfile.name )): - if line and not line.startswith( '#' ): - line = line.rstrip( '\r\n' ) - try: - fields = line.split("\t") - item = fields[group_col] - if ignorecase == 1: - item = item.lower() - if prev_item != "": - # At this level, we're grouping on values (item and prev_item) in group_col - if item == prev_item: - # Keep iterating and storing values until a new value is encountered. - for i, col in enumerate(cols): - col = int(col)-1 - valid = True - # Before appending the current value, make sure it is numeric if the - # operation for the column requires it. - if ops[i] not in str_ops: - try: - float( fields[col].strip()) - except: - valid = False - skipped_lines += 1 - if not first_invalid_line: - first_invalid_line = ii+1 - invalid_value = fields[col] - invalid_column = col+1 - if valid: - prev_vals[i].append(fields[col].strip()) - else: - """ - When a new value is encountered, write the previous value and the - corresponding aggregate values into the output file. This works - due to the sort on group_col we've applied to the data above. - """ - out_str = prev_item - multiple_modes = False - mode_index = None - for i, op in enumerate( ops ): - if op == 'cuniq': - rfunc = "r.c" - else: - rfunc = "r." + op - if op not in str_ops: - for j, elem in enumerate( prev_vals[i] ): - prev_vals[i][j] = float( elem ) - rout = eval( rfunc )( prev_vals[i] ) - if rounds[i] == 'yes': - rout = int(round(float(rout))) - else: - rout = '%g' %(float(rout)) - else: - if op != 'random': - rout = eval( rfunc )( prev_vals[i] ) - else: - try: - rand_index = random.randint(0,len(prev_vals[i])-1) #if the two inputs to randint are equal, it seems to throw a ValueError. This can't be reproduced with the python interpreter in its interactive mode. - except Exception, ValueError: - rand_index = 0 - rout = prev_vals[i][rand_index] - - if op == 'Mode' and rout == '>1 mode': - multiple_modes = True - mode_index = i - if op == 'unique': - rfunc = "r.length" - rout = eval( rfunc )( rout ) - if op in ['c', 'cuniq']: - if op == 'c': - if type(rout) == type([]): - out_str += "\t" + ','.join(rout) - else: - out_str += "\t" + str(rout) - else: - if type(rout) == type([]): - out_str += "\t" + ','.join(list(set(rout))) - else: - out_str += "\t" + str(rout) - else: - out_str += "\t" + str(rout) - if multiple_modes and mode_index != None: - out_str_list = out_str.split('\t') - for val in prev_vals[mode_index]: - out_str = '\t'.join(out_str_list[:mode_index+1]) + '\t' + str(val) + '\t' + '\t'.join(out_str_list[mode_index+2:]) - print >>fout, out_str.rstrip('\t') - else: - print >>fout, out_str - - prev_item = item - prev_vals = [] - for col in cols: - col = int(col)-1 - val_list = [] - val_list.append(fields[col].strip()) - prev_vals.append(val_list) - else: - # This only occurs once, right at the start of the iteration. - prev_item = item - for col in cols: - col = int(col)-1 - val_list = [] - val_list.append(fields[col].strip()) - prev_vals.append(val_list) - - except Exception, exc: - skipped_lines += 1 - if not first_invalid_line: - first_invalid_line = ii+1 - else: - skipped_lines += 1 - if not first_invalid_line: - first_invalid_line = ii+1 - - # Handle the last grouped value - out_str = prev_item - multiple_modes = False - mode_index = None - for i, op in enumerate(ops): - if op == 'cuniq': - rfunc = "r.c" - else: - rfunc = "r." + op - try: + def is_new_item(line): + item = line.strip().split("\t")[group_col] + if ignorecase == 1: + item = item.lower() + return item + + for key, line_list in groupby(tmpfile, key=is_new_item): + op_vals = [ [] for op in cols ] + out_str = key + multiple_modes = False + mode_index = None + + for line in line_list: + fields = line.strip().split("\t") + for i, col in enumerate(cols): + col = int(col)-1 # cXX from galaxy is 1-based + val = fields[col].strip() + # Before appending the current value, make sure it is numeric if the + # operation for the column requires it. + if ops[i] not in str_ops: + try: + float(val) + except ValueError: + skipped_lines += 1 + if first_invalid_line is None: + first_invalid_line = i+1 + invalid_value = fields[col] + invalid_column = col+1 + break + + op_vals[i].append(val) + + for i, op in enumerate( ops ): + if op == 'cuniq': + rfunc = "r.c" + else: + rfunc = "r." + op if op not in str_ops: - for j, elem in enumerate( prev_vals[i] ): - prev_vals[i][j] = float( elem ) - rout = eval( rfunc )( prev_vals[i] ) + for j, elem in enumerate( op_vals[i] ): + op_vals[i][j] = float( elem ) + rout = eval( rfunc )( op_vals[i] ) if rounds[i] == 'yes': - rout = int(round(float(rout))) + rout = round(float(rout)) else: rout = '%g' %(float(rout)) else: if op != 'random': - rout = eval( rfunc )( prev_vals[i] ) + rout = eval( rfunc )( op_vals[i] ) else: try: - rand_index = random.randint(0,len(prev_vals[i])-1) #if the two inputs to randint are equal, it seems to throw a ValueError. This can't be reproduced with the python interpreter in its interactive mode. - except Exception, ValueError: + rand_index = random.randint(0,len(op_vals[i])-1) #if the two inputs to randint are equal, it seems to throw a ValueError. This can't be reproduced with the python interpreter in its interactive mode. + except: rand_index = 0 - rout = prev_vals[i][rand_index] + rout = op_vals[i][rand_index] if op == 'Mode' and rout == '>1 mode': multiple_modes = True - mode_index = i + mode_index = i if op == 'unique': rfunc = "r.length" - rout = eval( rfunc )( rout ) - if op in ['c','cuniq']: - if op == 'c': - if type(rout) == type([]): - out_str += "\t" + ','.join(rout) - else: - out_str += "\t" + str(rout) + rout = eval( rfunc )( rout ) + if op in ['c', 'cuniq']: + if isinstance(rout, list): + if op == 'cuniq': + rout = set(rout) + out_str += "\t" + ','.join(rout) else: - if type(rout) == type([]): - out_str += "\t" + ','.join(list(set(rout))) - else: - out_str += "\t" + str(rout) + out_str += "\t" + str(rout) else: - out_str += "\t" + str( rout ) - except: - skipped_lines += 1 - if not first_invalid_line: - first_invalid_line = ii+1 - - if multiple_modes and mode_index != None: - out_str_list = out_str.split('\t') - for val in prev_vals[mode_index]: - out_str = '\t'.join(out_str_list[:mode_index+1]) + '\t' + str(val) + '\t' + '\t'.join(out_str_list[mode_index+2:]) - print >>fout, out_str.rstrip('\t') - else: - print >>fout, out_str + out_str += "\t" + str(rout) + if multiple_modes and mode_index != None: + out_str_list = out_str.split('\t') + for val in op_vals[mode_index]: + out_str = '\t'.join(out_str_list[:mode_index+1]) + '\t' + str(val) + '\t' + '\t'.join(out_str_list[mode_index+2:]) + fout.write(out_str.rstrip('\t') + "\n") + else: + fout.write(out_str + "\n") # Generate a useful info message. msg = "--Group by c%d: " %(group_col+1) - for i,op in enumerate(ops): + for i, op in enumerate(ops): if op == 'c': op = 'concat' elif op == 'length': --- a/tools/stats/grouping.xml Tue Mar 22 14:08:32 2011 -0400 +++ b/tools/stats/grouping.xml Tue Mar 22 17:49:09 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="Grouping1" name="Group" version="1.9.3"> +<tool id="Grouping1" name="Group" version="1.9.4"><description>data by a column and perform aggregate operation on other columns.</description><command interpreter="python"> grouping.py Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: fubar: Adding two new tool wrappers and tests - clustalw (http://www.clustal.org) for multiple alignments and a sequence motif generator based on weblogo3 (http://weblogo.berkeley.edu) which works on fasta files such as alignments from clustalw
by Bitbucket 22 Mar '11

22 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0319becf5e76/ changeset: r5246:0319becf5e76 user: fubar date: 2011-03-22 19:08:32 summary: Adding two new tool wrappers and tests - clustalw (http://www.clustal.org) for multiple alignments and a sequence motif generator based on weblogo3 (http://weblogo.berkeley.edu) which works on fasta files such as alignments from clustalw affected #: 8 files (155 bytes) --- a/tool_conf.xml.sample Tue Mar 22 13:45:31 2011 -0400 +++ b/tool_conf.xml.sample Tue Mar 22 14:08:32 2011 -0400 @@ -204,6 +204,10 @@ </section><section name="Motif Tools" id="motifs"><tool file="meme/meme.xml"/> + <tool file="rgenetics/rgWebLogo3.xml" /> + </section> + <section name="Multiple Alignments" id="clustal"> + <tool file="rgenetics/rgClustalw.xml" /></section><section name="Metagenomic analyses" id="tax_manipulation"><tool file="taxonomy/gi2taxonomy.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: richard_burhans: fixed comment bug and added additional error messages for SIFT tool
by Bitbucket 22 Mar '11

22 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/1113dcc5aaa7/ changeset: r5245:1113dcc5aaa7 user: richard_burhans date: 2011-03-22 18:45:31 summary: fixed comment bug and added additional error messages for SIFT tool affected #: 1 file (2.0 KB) --- a/tools/human_genome_variation/sift_variants_wrapper.sh Tue Mar 22 10:50:27 2011 -0400 +++ b/tools/human_genome_variation/sift_variants_wrapper.sh Tue Mar 22 13:45:31 2011 -0400 @@ -16,10 +16,48 @@ sift_input="$working_dir/sift_input.txt" sift_output="$working_dir/sift_output.txt" +################################################################################ +## make sure input file column selections are mutually exclusive ## +################################################################################ +ERROR=0 +declare -a col_use -## -## get/check the db directory from the argument org,db_loc -## +function check_col () { + local col=$1 + local use=$2 + local int=$3 + + if [ -n "${col//[0-9]}" ]; then + if [ $int -eq 1 ]; then + echo "ERROR: invalid value for $use column: $col" 1>&2 + ERROR=1 + fi + return + fi + + local cur=${col_use[$col]} + if [ -n "$cur" ]; then + echo "ERROR: $use column is the same as $cur column" 1>&2 + col_use[$col]="${cur},$use" + ERROR=1 + else + col_use[$col]=$use + fi +} + +check_col $chrom_col 'chromosome' 1 +check_col $pos_col 'position' 1 +check_col $allele_col 'allele' 1 +check_col $strand_col 'strand' 0 +check_col $comment_col 'comment' 0 + +if [ $ERROR -ne 0 ]; then + exit 1 +fi + +################################################################################ +## get/check the db directory from the argument org,db_loc ## +################################################################################ db_dir=$( awk '$1 == org { print $2 }' org=$org $db_loc ) if [ -z "$db_dir" ]; then @@ -32,9 +70,9 @@ exit 1 fi -## -## create input file for SIFT_exome_nssnvs.pl -## +################################################################################ +## create input file for SIFT_exome_nssnvs.pl ## +################################################################################ if [ ! -r "$input_file" ]; then echo "Can't read input file \"$input_file\"" 1>&2 exit 1 @@ -57,32 +95,26 @@ strand='"-1"' else strand="\$$strand_col" - strand_cvt='if ( '"${strand}"' == "+") { '"${strand}"' = "1" } else if ( '"${strand}"' == "-") { '"${strand}"' = "-1"}' + strand_cvt='if ('"${strand}"' == "+") {'"${strand}"' = "1"} else if ('"${strand}"' == "-") {'"${strand}"' = "-1"}' fi -if [ "$comment_col" = "-" ]; then - is_comment=0 -else - is_comment=1 +print_row='print $'"${chrom_col}"', $'"${beg_col}"', $'"${end_col}"', '"${strand}"', $'"${allele_col}"'' +if [ "$comment_col" != "-" ]; then + print_row=''"${print_row}"', $'"${comment_col}"'' fi awk ' BEGIN {FS="\t";OFS=","} +$'"${chrom_col}"' ~ /^[cC][hH][rR]/ {$'"${chrom_col}"' = substr($'"${chrom_col}"',4)} { - $'"${chrom_col}"' = tolower($'"${chrom_col}"') - sub(/^chr/, "", $'"${chrom_col}"') '"${strand_cvt}"' - if ('"${is_comment}"') { - print $'"${chrom_col}"', $'"${beg_col}"', $'"${end_col}"', '"${strand}"', $'"${allele_col}"', $'"${comment_col}"' - } else { - print $'"${chrom_col}"', $'"${beg_col}"', $'"${end_col}"', '"${strand}"', $'"${allele_col}"' - } + '"${print_row}"' } ' "$input_file" > "$sift_input" -## -## run SIFT variants command line program -## +################################################################################ +## run SIFT_exome_nssnvs.pl command line program ## +################################################################################ if [ "$output_opts" = "None" ]; then output_opts="" else @@ -92,18 +124,18 @@ SIFT_exome_nssnvs.pl -i "$sift_input" -d "$db_dir" -o "$working_dir" $output_opts &> "$sift_output" if [ $? -ne 0 ]; then - echo "failed: SIFT_exome_nssnvs.pl -i \"$sift_input\" -d \"$db_dir\" -o \"$working_dir\" $output_opts" - exit 1 + echo "failed: SIFT_exome_nssnvs.pl -i \"$sift_input\" -d \"$db_dir\" -o \"$working_dir\" $output_opts" + exit 1 fi -## -## locate the output file -## +################################################################################ +## locate the SIFT_exome_nssnvs.pl output file ## +################################################################################ sift_pid=$( sed -n -e 's/^.*Your job id is $[0-9][0-9]*$ and is currently running.*$/\1/p' "$sift_output" ) if [ -z "$sift_pid" ]; then - echo "Can't find SIFT pid in \"$sift_output\"" 1>&2 - exit 1 + echo "Can't find SIFT pid in \"$sift_output\"" 1>&2 + exit 1 fi sift_outdir="$working_dir/$sift_pid" @@ -118,9 +150,9 @@ exit 1 fi -## -## create output file -## +################################################################################ +## create galaxy output file ## +################################################################################ awk ' BEGIN {FS="\t";OFS="\t"} NR == 1 { @@ -139,14 +171,14 @@ print "#" $0 } NR != 1 { - if ($3 == "1") { $3 = "+" } else if ($3 == "-1") { $3 = "-" } + if ($3 == "1") {$3 = "+"} else if ($3 == "-1") {$3 = "-"} '"${pos_adj}"' print } ' > "$output_file" -## -## cleanup -## +################################################################################ +## cleanup ## +################################################################################ rm -rf "$sift_outdir" "$sift_input" "$sift_output" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix for bug introduced in change set 5243:45b772580403.
by Bitbucket 22 Mar '11

22 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/47f813d8cd6a/ changeset: r5244:47f813d8cd6a user: greg date: 2011-03-22 15:50:27 summary: Fix for bug introduced in change set 5243:45b772580403. affected #: 1 file (0 bytes) --- a/lib/galaxy/web/controllers/user.py Tue Mar 22 10:33:42 2011 -0400 +++ b/lib/galaxy/web/controllers/user.py Tue Mar 22 10:50:27 2011 -0400 @@ -494,7 +494,7 @@ else: status = 'error' if webapp == 'galaxy': - user_type_form_definition = self.__get_user_type_form_definition( trans, user=user, **kwd ) + user_type_form_definition = self.__get_user_type_form_definition( trans, user=None, **kwd ) user_type_fd_id = params.get( 'user_type_fd_id', 'none' ) if user_type_fd_id == 'none' and user_type_form_definition is not None: user_type_fd_id = trans.security.encode_id( user_type_form_definition.id ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 21 Mar '11

21 Mar '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ca9a43ca12f5/ changeset: r5241:ca9a43ca12f5 user: jgoecks date: 2011-03-21 18:01:24 summary: Add count GFF features tool and tests. Tool counts the number of features in a GFF file; this is different than the number of lines b/c GFF features are often multiline. affected #: 5 files (1.5 KB) --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count_gff_features_out1.txt Mon Mar 21 13:01:24 2011 -0400 @@ -0,0 +1,1 @@ +3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count_gff_features_out2.txt Mon Mar 21 13:01:24 2011 -0400 @@ -0,0 +1,1 @@ +14 --- a/tool_conf.xml.sample Mon Mar 21 11:08:32 2011 -0400 +++ b/tool_conf.xml.sample Mon Mar 21 13:01:24 2011 -0400 @@ -142,6 +142,8 @@ <tool file="stats/plot_from_lda.xml" /><tool file="regVariation/t_test_two_samples.xml" /><tool file="regVariation/compute_q_values.xml" /> + <label text="GFF" id="gff" /> + <tool file="stats/count_gff_features.xml" /></section><section name="Wavelet Analysis" id="dwt"><tool file="discreteWavelet/execute_dwt_IvC_all.xml" /> --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/stats/count_gff_features.py Mon Mar 21 13:01:24 2011 -0400 @@ -0,0 +1,18 @@ +#!/usr/bin/env python +# This tool takes a gff file as input and counts the number of features in it. + +import sys, fileinput +from galaxy import eggs +from galaxy.datatypes.util.gff_util import GFFReaderWrapper +from bx.intervals.io import GenomicInterval + +# Get args. +input_file = sys.argv[1:] + +# Count features. +count = 0 +for feature in GFFReaderWrapper( fileinput.FileInput( input_file ), fix_strand=True ): + if isinstance( feature, GenomicInterval ): + count += 1 + +print count \ No newline at end of file --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/stats/count_gff_features.xml Mon Mar 21 13:01:24 2011 -0400 @@ -0,0 +1,26 @@ +<tool id="count_gff_features" name="Count GFF Features" version="0.1"> + <description></description> + <command interpreter="python"> + count_gff_features.py $input > $output + </command> + <inputs> + <param format="gff" name="input" type="data" label="GFF Dataset to Filter"/> + </inputs> + <outputs> + <data format="txt" name="output"/> + </outputs> + <tests> + <test> + <param name="input" value="gff2bed_in2.gff"/> + <output name="output" file="count_gff_features_out1.txt"/> + </test> + <test> + <param name="input" value="gff_filter_by_feature_count_out1.gff"/> + <output name="output" file="count_gff_features_out2.txt"/> + </test> + </tests> + <help> + Counts the number of features in a GFF dataset. GFF features are often spread across multiple lines; this tool counts the number of + features in dataset rather than the number of lines. + </help> +</tool> http://bitbucket.org/galaxy/galaxy-central/changeset/8d476956222e/ changeset: r5242:8d476956222e user: jgoecks date: 2011-03-21 20:24:05 summary: Merge. affected #: 0 files (0 bytes) --- a/tools/filters/trimmer.xml Mon Mar 21 13:01:24 2011 -0400 +++ b/tools/filters/trimmer.xml Mon Mar 21 15:24:05 2011 -0400 @@ -1,11 +1,11 @@ -<tool id="trimmer" name="Trim" version="0.0.1"> - <description>leading or trailing characters</description> +<tool id="trimmer" name="Trim" version="0.0.1"> + <description>leading or trailing characters</description><command interpreter="python"> - trimmer.py -a -f $input1 -c $col -s $start -e $end -i $ignore $fastq > $out_file1 - </command> - <inputs> + trimmer.py -a -f $input1 -c $col -s $start -e $end -i $ignore $fastq > $out_file1 + </command> + <inputs><param format="tabular,txt" name="input1" type="data" label="this dataset"/> - <param name="col" type="integer" value="0" label="Trim this column only" help="0 = process entire line" /> + <param name="col" type="integer" value="0" label="Trim this column only" help="0 = process entire line" /><param name="start" type="integer" size="10" value="1" label="Trim from the beginning to this position" help="1 = do not trim the beginning"/><param name="end" type="integer" size="10" value="0" label="Remove everything from this position to the end" help="0 = do not trim the end"/><param name="fastq" type="select" label="Is input dataset in fastq format?" help="If set to YES, the tool will not trim evenly numbered lines (0, 2, 4, etc...)"> @@ -30,9 +30,9 @@ <option value="94">^</option><option value="35">#</option></param> - </inputs> - <outputs> - <data name="out_file1" format="input" metadata_source="input1"/> + </inputs> + <outputs> + <data name="out_file1" format="input" metadata_source="input1"/></outputs><tests><test> @@ -55,42 +55,42 @@ </test></tests> - - <help> - - -**What it does** - -Trims specified number of characters from a dataset or its field (if dataset is tab-delimited). - ------ - -**Example 1** - -Trimming this dataset:: + + <help> + + +**What it does** + +Trims specified number of characters from a dataset or its field (if dataset is tab-delimited). + +----- + +**Example 1** + +Trimming this dataset:: 1234567890 - abcdefghijk - + abcdefghijk + by setting **Trim from the beginning to this position** to *2* and **Remove everything from this position to the end** to *6* will produce:: 23456 - bcdef + bcdef ----- -**Eaxmple 2** +**Example 2** Trimming column 2 of this dataset:: - bcde 12345 fghij 67890 - fghij 67890 abcde 12345 + abcde 12345 fghij 67890 + fghij 67890 abcde 12345 -by setting **Trim content of this column only** to *2*, **Trim from the beginning to this position** to *2*, and **Remove everything from this position to the end** to *4* will produce:: +by setting **Trim content of this column only** to *2*, **Trim from the beginning to this position** to *2*, and **Remove everything from this position to the end** to *4* will produce:: - abcde 234 fghij 67890 - fghij 789 abcde 12345 - + abcde 234 fghij 67890 + fghij 789 abcde 12345 + ----- **Trimming FASTQ datasets** @@ -111,10 +111,10 @@ **Note** that headers are skipped. -.. class:: warningmark - -**WARNING:** This tool will only work on properly formatted fastq datasets where (1) each read and quality string occupy one line and (2) '@' (read header) and "+" (quality header) lines are evenly numbered like in the above example. +.. class:: warningmark - - </help> -</tool> +**WARNING:** This tool will only work on properly formatted fastq datasets where (1) each read and quality string occupy one line and (2) '@' (read header) and "+" (quality header) lines are evenly numbered like in the above example. + + + </help> +</tool> --- a/tools/new_operations/join.xml Mon Mar 21 13:01:24 2011 -0400 +++ b/tools/new_operations/join.xml Mon Mar 21 15:24:05 2011 -0400 @@ -11,12 +11,12 @@ <param name="min" size="4" type="integer" value="1" help="(bp)"><label>with min overlap</label></param> - <param name="fill" type="select" label="Return"> - <option value="none">Only records that are joined (INNER JOIN)</option> - <option value="right">All records of first dataset (fill null with ".")</option> - <option value="left">All records of second dataset (fill null with ".")</option> - <option value="both">All records of both datasets (fill nulls with ".")</option> - </param> + <param name="fill" type="select" label="Return"> + <option value="none">Only records that are joined (INNER JOIN)</option> + <option value="right">All records of first dataset (fill null with ".")</option> + <option value="left">All records of second dataset (fill null with ".")</option> + <option value="both">All records of both datasets (fill nulls with ".")</option> + </param></inputs><outputs><data format="interval" name="output" metadata_source="input1" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: kanwei: Typos in tool confs
by Bitbucket 21 Mar '11

21 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5541018c4738/ changeset: r5240:5541018c4738 user: kanwei date: 2011-03-21 18:48:28 summary: Typos in tool confs affected #: 2 files (38 bytes) --- a/tools/filters/trimmer.xml Mon Mar 21 11:08:32 2011 -0400 +++ b/tools/filters/trimmer.xml Mon Mar 21 13:48:28 2011 -0400 @@ -1,11 +1,11 @@ -<tool id="trimmer" name="Trim" version="0.0.1"> - <description>leading or trailing characters</description> +<tool id="trimmer" name="Trim" version="0.0.1"> + <description>leading or trailing characters</description><command interpreter="python"> - trimmer.py -a -f $input1 -c $col -s $start -e $end -i $ignore $fastq > $out_file1 - </command> - <inputs> + trimmer.py -a -f $input1 -c $col -s $start -e $end -i $ignore $fastq > $out_file1 + </command> + <inputs><param format="tabular,txt" name="input1" type="data" label="this dataset"/> - <param name="col" type="integer" value="0" label="Trim this column only" help="0 = process entire line" /> + <param name="col" type="integer" value="0" label="Trim this column only" help="0 = process entire line" /><param name="start" type="integer" size="10" value="1" label="Trim from the beginning to this position" help="1 = do not trim the beginning"/><param name="end" type="integer" size="10" value="0" label="Remove everything from this position to the end" help="0 = do not trim the end"/><param name="fastq" type="select" label="Is input dataset in fastq format?" help="If set to YES, the tool will not trim evenly numbered lines (0, 2, 4, etc...)"> @@ -30,9 +30,9 @@ <option value="94">^</option><option value="35">#</option></param> - </inputs> - <outputs> - <data name="out_file1" format="input" metadata_source="input1"/> + </inputs> + <outputs> + <data name="out_file1" format="input" metadata_source="input1"/></outputs><tests><test> @@ -55,42 +55,42 @@ </test></tests> - - <help> - - -**What it does** - -Trims specified number of characters from a dataset or its field (if dataset is tab-delimited). - ------ - -**Example 1** - -Trimming this dataset:: + + <help> + + +**What it does** + +Trims specified number of characters from a dataset or its field (if dataset is tab-delimited). + +----- + +**Example 1** + +Trimming this dataset:: 1234567890 - abcdefghijk - + abcdefghijk + by setting **Trim from the beginning to this position** to *2* and **Remove everything from this position to the end** to *6* will produce:: 23456 - bcdef + bcdef ----- -**Eaxmple 2** +**Example 2** Trimming column 2 of this dataset:: - bcde 12345 fghij 67890 - fghij 67890 abcde 12345 + abcde 12345 fghij 67890 + fghij 67890 abcde 12345 -by setting **Trim content of this column only** to *2*, **Trim from the beginning to this position** to *2*, and **Remove everything from this position to the end** to *4* will produce:: +by setting **Trim content of this column only** to *2*, **Trim from the beginning to this position** to *2*, and **Remove everything from this position to the end** to *4* will produce:: - abcde 234 fghij 67890 - fghij 789 abcde 12345 - + abcde 234 fghij 67890 + fghij 789 abcde 12345 + ----- **Trimming FASTQ datasets** @@ -111,10 +111,10 @@ **Note** that headers are skipped. -.. class:: warningmark - -**WARNING:** This tool will only work on properly formatted fastq datasets where (1) each read and quality string occupy one line and (2) '@' (read header) and "+" (quality header) lines are evenly numbered like in the above example. +.. class:: warningmark - - </help> -</tool> +**WARNING:** This tool will only work on properly formatted fastq datasets where (1) each read and quality string occupy one line and (2) '@' (read header) and "+" (quality header) lines are evenly numbered like in the above example. + + + </help> +</tool> --- a/tools/new_operations/join.xml Mon Mar 21 11:08:32 2011 -0400 +++ b/tools/new_operations/join.xml Mon Mar 21 13:48:28 2011 -0400 @@ -11,12 +11,12 @@ <param name="min" size="4" type="integer" value="1" help="(bp)"><label>with min overlap</label></param> - <param name="fill" type="select" label="Return"> - <option value="none">Only records that are joined (INNER JOIN)</option> - <option value="right">All records of first dataset (fill null with ".")</option> - <option value="left">All records of second dataset (fill null with ".")</option> - <option value="both">All records of both datasets (fill nulls with ".")</option> - </param> + <param name="fill" type="select" label="Return"> + <option value="none">Only records that are joined (INNER JOIN)</option> + <option value="right">All records of first dataset (fill null with ".")</option> + <option value="left">All records of second dataset (fill null with ".")</option> + <option value="both">All records of both datasets (fill nulls with ".")</option> + </param></inputs><outputs><data format="interval" name="output" metadata_source="input1" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Added row id print and pre/post value prints to the migration script addressing form value errors.
by Bitbucket 21 Mar '11

21 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6ffd5bca9d84/ changeset: r5239:6ffd5bca9d84 user: dannon date: 2011-03-21 16:08:32 summary: Added row id print and pre/post value prints to the migration script addressing form value errors. affected #: 1 file (348 bytes) --- a/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py Fri Mar 18 15:23:27 2011 -0400 +++ b/lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py Mon Mar 21 11:08:32 2011 -0400 @@ -20,7 +20,6 @@ def _sniffnfix_pg9_hex(value): """ Sniff for and fix postgres 9 hex decoding issue - """ try: if value[0] == 'x': @@ -33,7 +32,6 @@ def upgrade(): print __doc__ metadata.reflect() - cmd = "SELECT form_values.id as id, form_values.content as field_values, form_definition.fields as fields " \ + " FROM form_definition, form_values " \ + " WHERE form_values.form_definition_id=form_definition.id " \ @@ -50,6 +48,12 @@ # content field is corrupted fields_list = from_json_string( _sniffnfix_pg9_hex( str( row['fields'] ) ) ) field_values_str = _sniffnfix_pg9_hex( str( row['field_values'] ) ) + try: + #Encoding errors? Just to be safe. + print "Attempting to fix row %s" % row['id'] + print "Prior to replacement: %s" % field_values_str + except: + pass field_values_dict = {} # look for each field name in the values and extract its value (string) for index in range( len(fields_list) ): @@ -84,10 +88,15 @@ json_values = to_json_string(field_values_dict) cmd = "UPDATE form_values SET content='%s' WHERE id=%i" %( json_values, int( row['id'] ) ) db_session.execute( cmd ) + try: + print "Post replacement: %s" % json_values + except: + pass if corrupted_rows: print 'Fixed %i corrupted rows.' % corrupted_rows else: print 'No corrupted rows found.' def downgrade(): - pass \ No newline at end of file + pass + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Fix bug in recently used tool submenu that was caused by changeset 4967:d6559b2d69fc
by Bitbucket 18 Mar '11

18 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4c5bf02bb0e8/ changeset: r5238:4c5bf02bb0e8 user: jgoecks date: 2011-03-18 20:23:27 summary: Fix bug in recently used tool submenu that was caused by changeset 4967:d6559b2d69fc affected #: 1 file (48 bytes) --- a/templates/root/tool_menu.mako Fri Mar 18 14:42:08 2011 -0400 +++ b/templates/root/tool_menu.mako Fri Mar 18 15:23:27 2011 -0400 @@ -199,10 +199,10 @@ var found_in_list = false; // Look for new tool in current list. If found, rearrange list to move tool to top. + var new_tool_info_id = new_tool_info.id.toLowerCase().replace(/[^a-z0-9_]/, "_") recently_used_elts.each( function(index) { var anchor = $(this).find("a"); - var tool_id = anchor.attr("id").split("-")[1]; - if (tool_id === new_tool_info.id) { + if (anchor.hasClass("link-" + new_tool_info_id)) { found_in_list = true; // If tool is first, do nothing. @@ -219,7 +219,7 @@ // If tool not in list, create new element, remove last element, and put new element first in list. if (!found_in_list) { new_tool_elt = $("<div class='toolTitle'> \ - <a id='link-" + new_tool_info.id + "' href='" + new_tool_info.link + "' target='" + + <a class='link-" + new_tool_info.id + "' href='" + new_tool_info.link + "' target='" + new_tool_info.target + "' minsizehint='" + new_tool_info.minsizehint + "'>" + new_tool_info.name + "</a> " + new_tool_info.description + " \ </div>"); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: fix feature track bugs so that intervals are correctly drawn as half-open.
by Bitbucket 18 Mar '11

18 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/622acea0a86b/ changeset: r5237:622acea0a86b user: jgoecks date: 2011-03-18 19:42:08 summary: Trackster: fix feature track bugs so that intervals are correctly drawn as half-open. affected #: 1 file (30 bytes) --- a/static/scripts/trackster.js Fri Mar 18 14:12:10 2011 -0400 +++ b/static/scripts/trackster.js Fri Mar 18 14:42:08 2011 -0400 @@ -2348,7 +2348,8 @@ var feature_uid = feature[0], feature_start = feature[1], - feature_end = feature[2], + // -1 b/c intervals are half-open. + feature_end = feature[2] - 1, feature_name = feature[3], f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ), @@ -2440,8 +2441,9 @@ for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) { var block = feature_blocks[k], block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ), - block_end = Math.ceil( Math.min(width, Math.max((block[1] - tile_low) * w_scale)) ); - + // -1 b/c intervals are half-open. + block_end = Math.ceil( Math.min(width, Math.max((block[1] - 1 - tile_low) * w_scale)) ); + // Skip drawing if block not on tile. if (block_start > block_end) { continue; } @@ -2453,8 +2455,7 @@ // If block intersects with thick region, draw block as thick. if (thick_start !== undefined && !(block_start > thick_end || block_end < thick_start) ) { var block_thick_start = Math.max(block_start, thick_start), - // -1 b/c intervals are half-open. - block_thick_end = Math.min(block_end, thick_end-1); + block_thick_end = Math.min(block_end, thick_end); ctx.fillRect(block_thick_start + left_offset, y_center + 1, block_thick_end - block_thick_start, thick_height); } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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