1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e66766f18a58/ Changeset: e66766f18a58 User: Dave Bouvier Date: 2013-10-10 22:12:52 Summary: Remove migrated tools that were somehow restored to tool_conf.xml.sample Affected #: 1 file diff -r ff76fd33b81cdde1fb270de688ec5e86488ba34d -r e66766f18a58e200391f28157d0993b35014b84d tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -1,12 +1,12 @@ -<?xml version="1.0"?> +<?xml version='1.0' encoding='utf-8'?><toolbox> - <section name="Get Data" id="getext"> - <tool file="data_source/upload.xml"/> + <section id="getext" name="Get Data"> + <tool file="data_source/upload.xml" /><tool file="data_source/ucsc_tablebrowser.xml" /><tool file="data_source/ucsc_tablebrowser_test.xml" /><tool file="data_source/ucsc_tablebrowser_archaea.xml" /><tool file="data_source/bx_browser.xml" /> - <tool file="data_source/ebi_sra.xml"/> + <tool file="data_source/ebi_sra.xml" /><tool file="data_source/microbial_import.xml" /><tool file="data_source/biomart.xml" /><tool file="data_source/biomart_test.xml" /> @@ -32,19 +32,19 @@ <tool file="genomespace/genomespace_importer.xml" /><tool file="validation/fix_errors.xml" /></section> - <section name="Send Data" id="send"> + <section id="send" name="Send Data"><tool file="data_destination/epigraph.xml" /><tool file="data_destination/epigraph_test.xml" /><tool file="genomespace/genomespace_exporter.xml" /></section> - <section name="ENCODE Tools" id="EncodeTools"> + <section id="EncodeTools" name="ENCODE Tools"><tool file="encode/gencode_partition.xml" /><tool file="encode/random_intervals.xml" /></section> - <section name="Lift-Over" id="liftOver"> + <section id="liftOver" name="Lift-Over"><tool file="extract/liftOver_wrapper.xml" /></section> - <section name="Text Manipulation" id="textutil"> + <section id="textutil" name="Text Manipulation"><tool file="filters/fixedValueColumn.xml" /><tool file="stats/column_maker.xml" /><tool file="filters/catWrapper.xml" /> @@ -65,25 +65,25 @@ <tool file="stats/dna_filtering.xml" /><tool file="new_operations/tables_arithmetic_operations.xml" /></section> - <section name="Filter and Sort" id="filter"> + <section id="filter" name="Filter and Sort"><tool file="stats/filtering.xml" /><tool file="filters/sorter.xml" /><tool file="filters/grep.xml" /> - <label text="GFF" id="gff" /> + <label id="gff" text="GFF" /><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" /></section> - <section name="Join, Subtract and Group" id="group"> + <section id="group" name="Join, Subtract and Group"><tool file="filters/joiner.xml" /> - <tool file="filters/compare.xml"/> - <tool file="new_operations/subtract_query.xml"/> + <tool file="filters/compare.xml" /> + <tool file="new_operations/subtract_query.xml" /><tool file="stats/grouping.xml" /><tool file="new_operations/column_join.xml" /></section> - <section name="Convert Formats" id="convert"> + <section id="convert" name="Convert Formats"><tool file="filters/axt_to_concat_fasta.xml" /><tool file="filters/axt_to_fasta.xml" /><tool file="filters/axt_to_lav.xml" /> @@ -95,39 +95,38 @@ <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" /><tool file="filters/wiggle_to_simple.xml" /><tool file="filters/sff_extractor.xml" /><tool file="filters/gtf2bedgraph.xml" /><tool file="filters/wig_to_bigwig.xml" /><tool file="filters/bed_to_bigbed.xml" /></section> - <section name="Extract Features" id="features"> + <section id="features" name="Extract Features"><tool file="filters/ucsc_gene_bed_to_exon_bed.xml" /></section> - <section name="Fetch Sequences" id="fetchSeq"> + <section id="fetchSeq" name="Fetch Sequences"><tool file="extract/extract_genomic_dna.xml" /></section> - <section name="Fetch Alignments" id="fetchAlign"> + <section id="fetchAlign" name="Fetch Alignments"><tool file="maf/interval2maf_pairwise.xml" /><tool file="maf/interval2maf.xml" /> - <tool file="maf/maf_split_by_species.xml"/> + <tool file="maf/maf_split_by_species.xml" /><tool file="maf/interval_maf_to_merged_fasta.xml" /> - <tool file="maf/genebed_maf_to_fasta.xml"/> - <tool file="maf/maf_stats.xml"/> - <tool file="maf/maf_thread_for_species.xml"/> - <tool file="maf/maf_limit_to_species.xml"/> - <tool file="maf/maf_limit_size.xml"/> - <tool file="maf/maf_by_block_number.xml"/> - <tool file="maf/maf_reverse_complement.xml"/> - <tool file="maf/maf_filter.xml"/> + <tool file="maf/genebed_maf_to_fasta.xml" /> + <tool file="maf/maf_stats.xml" /> + <tool file="maf/maf_thread_for_species.xml" /> + <tool file="maf/maf_limit_to_species.xml" /> + <tool file="maf/maf_limit_size.xml" /> + <tool file="maf/maf_by_block_number.xml" /> + <tool file="maf/maf_reverse_complement.xml" /> + <tool file="maf/maf_filter.xml" /></section> - <section name="Get Genomic Scores" id="scores"> + <section id="scores" name="Get Genomic Scores"><tool file="stats/wiggle_to_simple.xml" /><tool file="stats/aggregate_binned_scores_in_intervals.xml" /><tool file="extract/phastOdds/phastOdds_tool.xml" /></section> - <section name="Operate on Genomic Intervals" id="bxops"> + <section id="bxops" name="Operate on Genomic Intervals"><tool file="new_operations/intersect.xml" /><tool file="new_operations/subtract.xml" /><tool file="new_operations/merge.xml" /> @@ -141,21 +140,19 @@ <tool file="new_operations/flanking_features.xml" /><tool file="annotation_profiler/annotation_profiler.xml" /></section> - <section name="Statistics" id="stats"> + <section id="stats" name="Statistics"><tool file="stats/gsummary.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" /><tool file="stats/plot_from_lda.xml" /> - <tool file="regVariation/t_test_two_samples.xml" /> - <tool file="regVariation/compute_q_values.xml" /><tool file="stats/MINE.xml" /> - <label text="GFF" id="gff" /> + <label id="gff" text="GFF" /><tool file="stats/count_gff_features.xml" /></section> - <section name="Wavelet Analysis" id="dwt"> + <section id="dwt" name="Wavelet Analysis"><tool file="discreteWavelet/execute_dwt_var_perFeature.xml" /><!-- Keep this section/tools commented until all of the tools have functional tests @@ -165,11 +162,10 @@ <tool file="discreteWavelet/execute_dwt_var_perClass.xml" /> --></section> - <section name="Graph/Display Data" id="plots"> + <section id="plots" name="Graph/Display Data"><tool file="plotting/histogram2.xml" /><tool file="plotting/scatterplot.xml" /><tool file="plotting/bar_chart.xml" /> - <tool file="plotting/xy_plot.xml" /><tool file="plotting/boxplot.xml" /><tool file="visualization/GMAJ.xml" /><tool file="visualization/LAJ.xml" /> @@ -177,57 +173,48 @@ <tool file="maf/vcf_to_maf_customtrack.xml" /><tool file="mutation/visualize.xml" /></section> - <section name="Regional Variation" id="regVar"> + <section id="regVar" name="Regional Variation"><tool file="regVariation/windowSplitter.xml" /><tool file="regVariation/featureCounter.xml" /><tool file="regVariation/WeightedAverage.xml" /><tool file="regVariation/quality_filter.xml" /><tool file="regVariation/maf_cpg_filter.xml" /><tool file="regVariation/getIndels_2way.xml" /> - <tool file="regVariation/getIndels_3way.xml" /><tool file="regVariation/getIndelRates_3way.xml" /><tool file="regVariation/substitutions.xml" /><tool file="regVariation/substitution_rates.xml" /><tool file="regVariation/microsats_alignment_level.xml" /><tool file="regVariation/microsats_mutability.xml" /> - <tool file="regVariation/delete_overlapping_indels.xml" /> - <tool file="regVariation/compute_motifs_frequency.xml" /> - <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" /></section> - <section name="Multiple regression" id="multReg"> + <section id="multReg" name="Multiple regression"><tool file="regVariation/linear_regression.xml" /><tool file="regVariation/logistic_regression_vif.xml" /><tool file="regVariation/best_regression_subsets.xml" /><tool file="regVariation/rcve.xml" /><tool file="regVariation/partialR_square.xml" /></section> - <section name="Multivariate Analysis" id="multVar"> + <section id="multVar" name="Multivariate Analysis"><tool file="multivariate_stats/pca.xml" /><tool file="multivariate_stats/cca.xml" /><tool file="multivariate_stats/kpca.xml" /><tool file="multivariate_stats/kcca.xml" /></section> - <section name="Evolution" id="hyphy"> + <section id="hyphy" name="Evolution"><tool file="hyphy/hyphy_branch_lengths_wrapper.xml" /><tool file="hyphy/hyphy_nj_tree_wrapper.xml" /><tool file="hyphy/hyphy_dnds_wrapper.xml" /> - <tool file="evolution/mutate_snp_codon.xml" /><tool file="evolution/codingSnps.xml" /><tool file="evolution/add_scores.xml" /></section> - <section name="Motif Tools" id="motifs"> - <tool file="meme/meme.xml"/> - <tool file="meme/fimo.xml"/> + <section id="motifs" name="Motif Tools"> + <tool file="meme/meme.xml" /> + <tool file="meme/fimo.xml" /><tool file="rgenetics/rgWebLogo3.xml" /></section> - <section name="Multiple Alignments" id="clustal"> + <section id="clustal" name="Multiple Alignments"><tool file="rgenetics/rgClustalw.xml" /></section> - <section name="Metagenomic analyses" id="tax_manipulation"> + <section id="tax_manipulation" name="Metagenomic analyses"><tool file="taxonomy/gi2taxonomy.xml" /><tool file="taxonomy/t2t_report.xml" /><tool file="taxonomy/t2ps_wrapper.xml" /> @@ -235,38 +222,35 @@ <tool file="taxonomy/lca.xml" /><tool file="taxonomy/poisson2test.xml" /></section> - <section name="FASTA manipulation" id="fasta_manipulation"> + <section id="fasta_manipulation" name="FASTA manipulation"><tool file="fasta_tools/fasta_compute_length.xml" /><tool file="fasta_tools/fasta_filter_by_length.xml" /><tool file="fasta_tools/fasta_concatenate_by_species.xml" /><tool file="fasta_tools/fasta_to_tabular.xml" /><tool file="fasta_tools/tabular_to_fasta.xml" /> - <tool file="fastx_toolkit/fasta_formatter.xml" /> - <tool file="fastx_toolkit/fasta_nucleotide_changer.xml" /> - <tool file="fastx_toolkit/fastx_collapser.xml" /></section> - <section name="NGS: QC and manipulation" id="NGS_QC"> + <section id="NGS_QC" name="NGS: QC and manipulation"> - <label text="FastQC: fastq/sam/bam" id="fastqcsambam" /> + <label id="fastqcsambam" text="FastQC: fastq/sam/bam" /><tool file="rgenetics/rgFastQC.xml" /> - <label text="Illumina fastq" id="illumina" /> + <label id="illumina" text="Illumina fastq" /><tool file="fastq/fastq_groomer.xml" /><tool file="fastq/fastq_paired_end_splitter.xml" /><tool file="fastq/fastq_paired_end_joiner.xml" /><tool file="fastq/fastq_stats.xml" /> - <label text="Roche-454 data" id="454" /> + <label id="454" text="Roche-454 data" /><tool file="metag_tools/short_reads_figure_score.xml" /><tool file="metag_tools/short_reads_trim_seq.xml" /><tool file="fastq/fastq_combiner.xml" /> - <label text="AB-SOLiD data" id="solid" /> + <label id="solid" text="AB-SOLiD data" /><tool file="next_gen_conversion/solid2fastq.xml" /><tool file="solid_tools/solid_qual_stats.xml" /><tool file="solid_tools/solid_qual_boxplot.xml" /> - <label text="Generic FASTQ manipulation" id="generic_fastq" /> + <label id="generic_fastq" text="Generic FASTQ manipulation" /><tool file="fastq/fastq_filter.xml" /><tool file="fastq/fastq_trimmer.xml" /><tool file="fastq/fastq_trimmer_by_quality.xml" /> @@ -274,25 +258,10 @@ <tool file="fastq/fastq_paired_end_interlacer.xml" /><tool file="fastq/fastq_paired_end_deinterlacer.xml" /><tool file="fastq/fastq_manipulation.xml" /> - <tool file="fastq/fastq_to_fasta.xml" /><tool file="fastq/fastq_to_tabular.xml" /><tool file="fastq/tabular_to_fastq.xml" /> - <label text="FASTX-Toolkit for FASTQ data" id="fastx_toolkit" /> - <tool file="fastx_toolkit/fastq_quality_converter.xml" /> - <tool file="fastx_toolkit/fastx_quality_statistics.xml" /> - <tool file="fastx_toolkit/fastq_quality_boxplot.xml" /> - <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" /> - <tool file="fastx_toolkit/fastq_to_fasta.xml" /> - <tool file="fastx_toolkit/fastq_quality_filter.xml" /> - <tool file="fastx_toolkit/fastq_to_fasta.xml" /> - <tool file="fastx_toolkit/fastx_artifacts_filter.xml" /> - <tool file="fastx_toolkit/fastx_barcode_splitter.xml" /> - <tool file="fastx_toolkit/fastx_clipper.xml" /> - <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" /> + <label id="fastx_toolkit" text="FASTX-Toolkit for FASTQ data" /></section><!-- Keep this section commented until it includes tools that @@ -305,31 +274,26 @@ <tool file="sr_assembly/velveth.xml" /></section> --> - <section name="NGS: Mapping" id="solexa_tools"> + <section id="solexa_tools" name="NGS: Mapping"><tool file="sr_mapping/bowtie2_wrapper.xml" /><tool file="sr_mapping/bfast_wrapper.xml" /><tool file="metag_tools/megablast_wrapper.xml" /><tool file="metag_tools/megablast_xml_parser.xml" /><tool file="sr_mapping/PerM.xml" /><tool file="sr_mapping/srma_wrapper.xml" /> - <tool file="sr_mapping/mosaik.xml"/> + <tool file="sr_mapping/mosaik.xml" /></section> - <section name="NGS: Indel Analysis" id="indel_analysis"> + <section id="indel_analysis" name="NGS: Indel Analysis"><tool file="indels/sam_indel_filter.xml" /> - <tool file="indels/indel_sam2interval.xml" /><tool file="indels/indel_table.xml" /><tool file="indels/indel_analysis.xml" /></section> - <section name="NGS: RNA Analysis" id="ngs-rna-tools"> + <section id="ngs-rna-tools" name="NGS: RNA Analysis"> - <label text="RNA-seq" id="rna_seq" /> + <label id="rna_seq" text="RNA-seq" /><tool file="ngs_rna/tophat_wrapper.xml" /><tool file="ngs_rna/tophat2_wrapper.xml" /><tool file="ngs_rna/tophat_color_wrapper.xml" /> - <tool file="ngs_rna/cufflinks_wrapper.xml" /> - <tool file="ngs_rna/cuffcompare_wrapper.xml" /> - <tool file="ngs_rna/cuffmerge_wrapper.xml" /> - <tool file="ngs_rna/cuffdiff_wrapper.xml" /><tool file="ngs_rna/express_wrapper.xml" /><!-- Trinity is very memory-intensive and should only be enabled/run on instances with sufficient resources. @@ -337,87 +301,71 @@ <tool file="ngs_rna/trinity_all.xml" /> --> - <label text="Filtering" id="filtering" /> + <label id="filtering" text="Filtering" /><tool file="ngs_rna/filter_transcripts_via_tracking.xml" /></section> - <section name="NGS: SAM Tools" id="samtools"> - <tool file="samtools/sam_bitwise_flag_filter.xml" /> - <tool file="samtools/sam2interval.xml" /> - <tool file="samtools/sam_to_bam.xml" /> - <tool file="samtools/bam_to_sam.xml" /> - <tool file="samtools/sam_merge.xml" /> - <tool file="samtools/samtools_mpileup.xml" /> - <tool file="samtools/sam_pileup.xml" /> - <tool file="samtools/pileup_parser.xml" /> - <tool file="samtools/pileup_interval.xml" /> - <tool file="samtools/samtools_flagstat.xml" /> - <tool file="samtools/samtools_rmdup.xml" /> - <tool file="samtools/samtools_slice_bam.xml" /> + <section id="samtools" name="NGS: SAM Tools"></section> - <section name="NGS: GATK Tools (beta)" id="gatk"> - <label text="Alignment Utilities" id="gatk_bam_utilities"/> + <section id="gatk" name="NGS: GATK Tools (beta)"> + <label id="gatk_bam_utilities" text="Alignment Utilities" /><tool file="gatk/depth_of_coverage.xml" /><tool file="gatk/print_reads.xml" /> - <label text="Realignment" id="gatk_realignment" /> + <label id="gatk_realignment" text="Realignment" /><tool file="gatk/realigner_target_creator.xml" /><tool file="gatk/indel_realigner.xml" /> - <label text="Base Recalibration" id="gatk_recalibration" /> + <label id="gatk_recalibration" text="Base Recalibration" /><tool file="gatk/count_covariates.xml" /><tool file="gatk/table_recalibration.xml" /><tool file="gatk/analyze_covariates.xml" /> - <label text="Genotyping" id="gatk_genotyping" /> + <label id="gatk_genotyping" text="Genotyping" /><tool file="gatk/unified_genotyper.xml" /> - <label text="Annotation" id="gatk_annotation" /> + <label id="gatk_annotation" text="Annotation" /><tool file="gatk/variant_annotator.xml" /> - <label text="Filtration" id="gatk_filtration" /> + <label id="gatk_filtration" text="Filtration" /><tool file="gatk/variant_filtration.xml" /><tool file="gatk/variant_select.xml" /> - <label text="Variant Quality Score Recalibration" id="gatk_variant_quality_score_recalibration" /> + <label id="gatk_variant_quality_score_recalibration" text="Variant Quality Score Recalibration" /><tool file="gatk/variant_recalibrator.xml" /><tool file="gatk/variant_apply_recalibration.xml" /> - <label text="Variant Utilities" id="gatk_variant_utilities"/> + <label id="gatk_variant_utilities" text="Variant Utilities" /><tool file="gatk/variants_validate.xml" /><tool file="gatk/variant_eval.xml" /><tool file="gatk/variant_combine.xml" /></section> - <section name="NGS: Peak Calling" id="peak_calling"> + <section id="peak_calling" name="NGS: Peak Calling"><tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /><tool file="peak_calling/ccat_wrapper.xml" /><tool file="genetrack/genetrack_indexer.xml" /><tool file="genetrack/genetrack_peak_prediction.xml" /></section> - <section name="NGS: Simulation" id="ngs-simulation"> + <section id="ngs-simulation" name="NGS: Simulation"><tool file="ngs_simulation/ngs_simulation.xml" /></section> - <section name="Phenotype Association" id="hgv"> + <section id="hgv" name="Phenotype Association"><tool file="evolution/codingSnps.xml" /><tool file="evolution/add_scores.xml" /><tool file="phenotype_association/sift.xml" /><tool file="phenotype_association/linkToGProfile.xml" /> - <tool file="phenotype_association/linkToDavid.xml"/> - <tool file="phenotype_association/ctd.xml" /> - <tool file="phenotype_association/funDo.xml" /> + <tool file="phenotype_association/linkToDavid.xml" /><tool file="phenotype_association/snpFreq.xml" /><tool file="phenotype_association/ldtools.xml" /><tool file="phenotype_association/pass.xml" /><tool file="phenotype_association/gpass.xml" /><tool file="phenotype_association/beam.xml" /><tool file="phenotype_association/lps.xml" /> - <tool file="phenotype_association/hilbertvis.xml" /><tool file="phenotype_association/freebayes.xml" /><tool file="phenotype_association/master2pg.xml" /><tool file="phenotype_association/vcf2pgSnp.xml" /> - <tool file="phenotype_association/dividePgSnpAlleles.xml" /></section> - <section name="VCF Tools" id="vcf_tools"> + <section id="vcf_tools" name="VCF Tools"><tool file="vcf_tools/intersect.xml" /><tool file="vcf_tools/annotate.xml" /><tool file="vcf_tools/filter.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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