1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6206a27bd2ae/ changeset: 6206a27bd2ae branch: feature/ws user: trevorw date: 2011-07-22 22:17:26 summary: minor whitespace updates, tab/space consistency affected #: 4 files (122 bytes) --- a/datatypes_conf.xml.sample Fri Jul 22 10:15:37 2011 -0400 +++ b/datatypes_conf.xml.sample Fri Jul 22 15:17:26 2011 -0500 @@ -123,7 +123,7 @@ <datatype extension="vcf" type="galaxy.datatypes.tabular:Vcf" display_in_upload="true"><converter file="vcf_to_bgzip_converter.xml" target_datatype="bgzip"/><converter file="vcf_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> - <converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/> + <converter file="vcf_to_summary_tree_converter.xml" target_datatype="summary_tree"/></datatype><datatype extension="wsf" type="galaxy.datatypes.wsf:SnpFile" display_in_upload="true"/><datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/> @@ -274,10 +274,10 @@ </registration><sniffers><!-- - The order in which Galaxy attempts to determine data types is - important because some formats are much more loosely defined - than others. The following list should be the most rigidly - defined format first, followed by next-most rigidly defined, + The order in which Galaxy attempts to determine data types is + important because some formats are much more loosely defined + than others. The following list should be the most rigidly + defined format first, followed by next-most rigidly defined, and so on. --><sniffer type="galaxy.datatypes.tabular:Vcf"/> --- a/tool_conf.xml.main Fri Jul 22 10:15:37 2011 -0400 +++ b/tool_conf.xml.main Fri Jul 22 15:17:26 2011 -0500 @@ -51,7 +51,7 @@ <tool file="fasta_tools/fasta_to_tabular.xml" /><tool file="filters/gff2bed.xml" /><tool file="maf/maf_to_bed.xml" /> - <tool file="maf/maf_to_interval.xml" /> + <tool file="maf/maf_to_interval.xml" /><tool file="maf/maf_to_fasta.xml" /><tool file="fasta_tools/tabular_to_fasta.xml" /><tool file="fastq/fastq_to_fasta.xml" /> @@ -78,13 +78,13 @@ <tool file="filters/gff/extract_GFF_Features.xml" /><tool file="filters/gff/gff_filter_by_attribute.xml" /><tool file="filters/gff/gff_filter_by_feature_count.xml" /> - <tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" /> + <tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" /></section><section name="Join, Subtract and Group" id="group"><tool file="filters/joiner.xml" /><tool file="filters/compare.xml"/><tool file="new_operations/subtract_query.xml"/> - <tool file="stats/grouping.xml" /> + <tool file="stats/grouping.xml" /><tool file="new_operations/column_join.xml"/></section><section name="Extract Features" id="features"> @@ -112,7 +112,7 @@ <tool file="extract/phastOdds/phastOdds_tool.xml" /></section><section name="Operate on Genomic Intervals" id="bxops"> - <tool file="new_operations/intersect.xml" /> + <tool file="new_operations/intersect.xml" /><tool file="new_operations/subtract.xml" /><tool file="new_operations/merge.xml" /><tool file="new_operations/concat.xml" /> @@ -127,7 +127,7 @@ </section><section name="Statistics" id="stats"><tool file="stats/gsummary.xml" /> - <tool file="filters/uniq.xml" /> + <tool file="filters/uniq.xml" /><tool file="stats/cor.xml" /><tool file="stats/generate_matrix_for_pca_lda.xml" /><tool file="stats/lda_analy.xml" /> @@ -223,13 +223,13 @@ <tool file="emboss_5/emboss_chips.xml" /><tool file="emboss_5/emboss_cirdna.xml" /><tool file="emboss_5/emboss_codcmp.xml" /> - <tool file="emboss_5/emboss_coderet.xml" /> + <tool file="emboss_5/emboss_coderet.xml" /><tool file="emboss_5/emboss_compseq.xml" /> - <tool file="emboss_5/emboss_cpgplot.xml" /> + <tool file="emboss_5/emboss_cpgplot.xml" /><tool file="emboss_5/emboss_cpgreport.xml" /><tool file="emboss_5/emboss_cusp.xml" /><tool file="emboss_5/emboss_cutseq.xml" /> - <tool file="emboss_5/emboss_dan.xml" /> + <tool file="emboss_5/emboss_dan.xml" /><tool file="emboss_5/emboss_degapseq.xml" /><tool file="emboss_5/emboss_descseq.xml" /><tool file="emboss_5/emboss_diffseq.xml" /> @@ -245,7 +245,7 @@ <tool file="emboss_5/emboss_etandem.xml" /><tool file="emboss_5/emboss_extractfeat.xml" /><tool file="emboss_5/emboss_extractseq.xml" /> - <tool file="emboss_5/emboss_freak.xml" /> + <tool file="emboss_5/emboss_freak.xml" /><tool file="emboss_5/emboss_fuzznuc.xml" /><tool file="emboss_5/emboss_fuzzpro.xml" /><tool file="emboss_5/emboss_fuzztran.xml" /> @@ -266,7 +266,7 @@ <tool file="emboss_5/emboss_merger.xml" /><tool file="emboss_5/emboss_msbar.xml" /><tool file="emboss_5/emboss_needle.xml" /> - <tool file="emboss_5/emboss_newcpgreport.xml" /> + <tool file="emboss_5/emboss_newcpgreport.xml" /><tool file="emboss_5/emboss_newcpgseek.xml" /><tool file="emboss_5/emboss_newseq.xml" /><tool file="emboss_5/emboss_noreturn.xml" /> @@ -294,7 +294,7 @@ <tool file="emboss_5/emboss_revseq.xml" /><tool file="emboss_5/emboss_seqmatchall.xml" /><tool file="emboss_5/emboss_seqret.xml" /> - <tool file="emboss_5/emboss_showfeat.xml" /> + <tool file="emboss_5/emboss_showfeat.xml" /><tool file="emboss_5/emboss_shuffleseq.xml" /><tool file="emboss_5/emboss_sigcleave.xml" /><tool file="emboss_5/emboss_sirna.xml" /> @@ -316,7 +316,7 @@ <tool file="emboss_5/emboss_water.xml" /><tool file="emboss_5/emboss_wobble.xml" /><tool file="emboss_5/emboss_wordcount.xml" /> - <tool file="emboss_5/emboss_wordmatch.xml" /> + <tool file="emboss_5/emboss_wordmatch.xml" /></section><label text="NGS Toolbox Beta" id="ngs" /><section name="NGS: QC and manipulation" id="cshl_library_information"> --- a/tool_conf.xml.sample Fri Jul 22 10:15:37 2011 -0400 +++ b/tool_conf.xml.sample Fri Jul 22 15:17:26 2011 -0500 @@ -144,14 +144,14 @@ <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" /> + <tool file="stats/count_gff_features.xml" /></section><!-- Keep this section commented until all of the tools have functional tests <section name="Wavelet Analysis" id="dwt"><tool file="discreteWavelet/execute_dwt_IvC_all.xml" /><tool file="discreteWavelet/execute_dwt_cor_aVa_perClass.xml" /> - <tool file="discreteWavelet/execute_dwt_cor_aVb_all.xml" /> + <tool file="discreteWavelet/execute_dwt_cor_aVb_all.xml" /><tool file="discreteWavelet/execute_dwt_var_perClass.xml" /></section> --> @@ -184,8 +184,8 @@ <tool file="regVariation/compute_motif_frequencies_for_all_motifs.xml" /><tool file="regVariation/categorize_elements_satisfying_criteria.xml" />s <tool file="regVariation/draw_stacked_barplots.xml" /> - <tool file="regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml" /> - <tool file="regVariation/microsatellite_birthdeath.xml" /> + <tool file="regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml" /> + <tool file="regVariation/microsatellite_birthdeath.xml" /></section><section name="Multiple regression" id="multReg"><tool file="regVariation/linear_regression.xml" /> @@ -241,7 +241,7 @@ </section><section name="NGS: QC and manipulation" id="NGS_QC"><label text="FastQC: fastq/sam/bam" id="fastqcsambam" /> - <tool file="rgenetics/rgFastQC.xml" /> + <tool file="rgenetics/rgFastQC.xml" /><label text="Illumina fastq" id="illumina" /><tool file="fastq/fastq_groomer.xml" /><tool file="fastq/fastq_paired_end_splitter.xml" /> @@ -280,21 +280,21 @@ <tool file="fastx_toolkit/fastx_collapser.xml" /><tool file="fastx_toolkit/fastx_renamer.xml" /><tool file="fastx_toolkit/fastx_reverse_complement.xml" /> - <tool file="fastx_toolkit/fastx_trimmer.xml" /> + <tool file="fastx_toolkit/fastx_trimmer.xml" /></section><section name="NGS: Picard (beta)" id="picard_beta"><label text="QC/Metrics for sam/bam" id="qcsambam"/><tool file="picard/picard_BamIndexStats.xml" /> - <tool file="picard/rgPicardASMetrics.xml" /> - <tool file="picard/rgPicardGCBiasMetrics.xml" /> - <tool file="picard/rgPicardLibComplexity.xml" /> + <tool file="picard/rgPicardASMetrics.xml" /> + <tool file="picard/rgPicardGCBiasMetrics.xml" /> + <tool file="picard/rgPicardLibComplexity.xml" /><tool file="picard/rgPicardInsertSize.xml" /><tool file="picard/rgPicardHsMetrics.xml" /><label text="bam/sam Cleaning" id="picard-clean" /><tool file="picard/picard_AddOrReplaceReadGroups.xml" /><tool file="picard/picard_ReorderSam.xml" /><tool file="picard/picard_ReplaceSamHeader.xml" /> - <tool file="picard/rgPicardFixMate.xml" /> + <tool file="picard/rgPicardFixMate.xml" /><tool file="picard/rgPicardMarkDups.xml" /></section><!-- --- a/tool_list.py Fri Jul 22 10:15:37 2011 -0400 +++ b/tool_list.py Fri Jul 22 15:17:26 2011 -0500 @@ -4,19 +4,19 @@ onoff = 1 tool_list = [] for line in open("tool_conf.xml.sample", "r"): - if line.find("<!--") != -1: + if line.find("<!--") != -1: onoff = 0 - if line.find("file") != -1 and onoff==1: - strs = line.split('\"') + if line.find("file") != -1 and onoff==1: + strs = line.split('\"') tool_list.append(strs[1]) - if line.find("<section") != -1 and onoff==1: + if line.find("<section") != -1 and onoff==1: keys = line.strip().split('\"') n = 0 strtmp = "section::" - while n < len(keys) : - if keys[n].find("id") != -1 : strtmp = strtmp + keys[n+1] - if keys[n].find("name") != -1 : strtmp = strtmp + keys[n+1] + "-" - n = n + 1 + while n < len(keys) : + if keys[n].find("id") != -1 : strtmp = strtmp + keys[n+1] + if keys[n].find("name") != -1 : strtmp = strtmp + keys[n+1] + "-" + n = n + 1 tool_list.append(strtmp.replace(' ', '_')) if line.find("-->") != -1: onoff =1 @@ -26,42 +26,42 @@ id = [] desc = [] tool_infos = [] -for tool in tool_list : - if tool.find("section")!=-1 : +for tool in tool_list : + if tool.find("section")!=-1 : tool_info = dict() tool_info["id"] = tool tool_infos.append(tool_info) - if os.path.exists("tools/"+tool) : - for line in open("tools/"+tool) : - if line.find("<tool ") != -1 and line.find("id") != -1 : - keys = line.strip().split('\"') - n = 0 - tool_info = dict() - tool_info["desc"] = '' - while n < len(keys) : - if keys[n].find("id") != -1 : tool_info["id"] = keys[n+1].replace(' ', '_') - if keys[n].find("name") != -1 : tool_info["name"] = keys[n+1] - if keys[n].find("description") != -1 : tool_info["desc"] = keys[n+1] - n = n + 1 - tool_infos.append(tool_info) - break + if os.path.exists("tools/"+tool) : + for line in open("tools/"+tool) : + if line.find("<tool ") != -1 and line.find("id") != -1 : + keys = line.strip().split('\"') + n = 0 + tool_info = dict() + tool_info["desc"] = '' + while n < len(keys) : + if keys[n].find("id") != -1 : tool_info["id"] = keys[n+1].replace(' ', '_') + if keys[n].find("name") != -1 : tool_info["name"] = keys[n+1] + if keys[n].find("description") != -1 : tool_info["desc"] = keys[n+1] + n = n + 1 + tool_infos.append(tool_info) + break flag=0 -if len(sys.argv) == 1 : - for tool_info in tool_infos: - if tool_info["id"].find("section") != -1 : +if len(sys.argv) == 1 : + for tool_info in tool_infos: + if tool_info["id"].find("section") != -1 : print "===========================================================================================================================================" print "%-45s\t%-40s\t%s" % ("id", "name", tool_info["id"]) print "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -" else : print "%-45s\t%-40s" % (tool_info["id"], tool_info["name"]) -else: - for tool_info in tool_infos: +else: + for tool_info in tool_infos: if tool_info["id"].find("section") != -1 : flag=0 elif flag==1: print " functional.test_toolbox:TestForTool_%s" % tool_info["id"], - if tool_info["id"].replace('section::', '')==sys.argv[1]: + if tool_info["id"].replace('section::', '')==sys.argv[1]: flag=1 #for key in tool_infos.keys(): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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