From b0efe4ddea45371c6ab02263c280cccc2f8fb4b0 Mon Sep 17 00:00:00 2001 From: Dave Bouvier Date: Thu, 26 Sep 2013 10:05:00 -0400 Subject: [PATCH] Migrate tools from the distribution to the tool shed, including but not limited to samtools and fastx_toolkit tools. --- .../migrate/versions/0008_tools.py | 106 + scripts/migrate_tools/0008_tools.sh | 4 + scripts/migrate_tools/0008_tools.xml | 135 + test-data/1.bam | Bin 3592 -> 0 bytes test-data/3unsorted.bam | Bin 1666 -> 0 bytes test-data/pileup_parser.6col.pileup | 1000 --- tool_conf.xml.sample | 190 +- tools/evolution/mutate_snp_codon.py | 112 - tools/evolution/mutate_snp_codon.xml | 67 - .../fasta_clipping_histogram.xml | 110 - tools/fastx_toolkit/fasta_formatter.xml | 87 - .../fasta_nucleotide_changer.xml | 73 - tools/fastx_toolkit/fastq_quality_boxplot.xml | 56 - .../fastx_toolkit/fastq_quality_converter.xml | 97 - tools/fastx_toolkit/fastq_quality_filter.xml | 82 - tools/fastx_toolkit/fastq_to_fasta.xml | 80 - .../fastx_toolkit/fastx_artifacts_filter.xml | 90 - .../fastx_toolkit/fastx_barcode_splitter.xml | 76 - .../fastx_barcode_splitter_galaxy_wrapper.sh | 80 - tools/fastx_toolkit/fastx_clipper.xml | 115 - tools/fastx_toolkit/fastx_collapser.xml | 88 - .../fastx_nucleotides_distribution.xml | 51 - .../fastx_quality_statistics.xml | 70 - tools/fastx_toolkit/fastx_renamer.xml | 65 - .../fastx_reverse_complement.xml | 63 - tools/fastx_toolkit/fastx_trimmer.xml | 81 - tools/phenotype_association/ctd.pl | 80 - tools/phenotype_association/ctd.xml | 289 - .../disease_ontology_gene_fuzzy_selector.pl | 64 - .../dividePgSnpAlleles.pl | 41 - .../dividePgSnpAlleles.xml | 76 - tools/phenotype_association/funDo.xml | 101 - tools/phenotype_association/hilbertvis.sh | 109 - tools/phenotype_association/hilbertvis.xml | 117 - tools/plotting/r_wrapper.sh | 23 - tools/plotting/xy_plot.xml | 148 - ...categorize_elements_satisfying_criteria.pl | 172 - ...ategorize_elements_satisfying_criteria.xml | 78 - ...ompute_motif_frequencies_for_all_motifs.pl | 153 - ...mpute_motif_frequencies_for_all_motifs.xml | 72 - .../regVariation/compute_motifs_frequency.pl | 252 - .../regVariation/compute_motifs_frequency.xml | 109 - .../regVariation/delete_overlapping_indels.pl | 94 - .../delete_overlapping_indels.xml | 66 - tools/regVariation/draw_stacked_barplots.pl | 78 - tools/regVariation/draw_stacked_barplots.xml | 59 - tools/regVariation/getIndels_3way.xml | 53 - .../regVariation/microsatellite_birthdeath.pl | 4333 ------------- .../microsatellite_birthdeath.xml | 104 - ...icrosatDataGenerator_interrupted_GALAXY.pl | 5606 ----------------- ...crosatDataGenerator_interrupted_GALAXY.xml | 93 - tools/regVariation/parseMAF_smallIndels.pl | 698 -- tools/regVariation/t_test_two_samples.pl | 109 - tools/regVariation/t_test_two_samples.xml | 160 - tools/samtools/bam_to_sam.py | 129 - tools/samtools/bam_to_sam.xml | 66 - tools/samtools/pileup_interval.py | 117 - tools/samtools/pileup_interval.xml | 189 - tools/samtools/pileup_parser.pl | 121 - tools/samtools/pileup_parser.xml | 387 -- tools/samtools/sam2interval.py | 96 - tools/samtools/sam2interval.xml | 72 - tools/samtools/sam_bitwise_flag_filter.py | 149 - tools/samtools/sam_bitwise_flag_filter.xml | 97 - tools/samtools/sam_merge.py | 74 - tools/samtools/sam_merge.xml | 62 - tools/samtools/sam_merge_code.py | 34 - tools/samtools/sam_pileup.py | 163 - tools/samtools/sam_pileup.xml | 190 - tools/samtools/sam_to_bam.py | 197 - tools/samtools/sam_to_bam.xml | 97 - tools/samtools/samtools_flagstat.xml | 37 - tools/samtools/samtools_mpileup.xml | 213 - tools/samtools/samtools_rmdup.xml | 69 - tools/samtools/samtools_slice_bam.py | 75 - tools/samtools/samtools_slice_bam.xml | 40 - tools/samtools/samtools_wrapper.py | 110 - 77 files changed, 316 insertions(+), 18783 deletions(-) create mode 100644 lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py create mode 100644 scripts/migrate_tools/0008_tools.sh create mode 100644 scripts/migrate_tools/0008_tools.xml delete mode 100644 test-data/1.bam delete mode 100644 test-data/3unsorted.bam delete mode 100644 test-data/pileup_parser.6col.pileup delete mode 100644 tools/evolution/mutate_snp_codon.py delete mode 100644 tools/evolution/mutate_snp_codon.xml delete mode 100644 tools/fastx_toolkit/fasta_clipping_histogram.xml delete mode 100644 tools/fastx_toolkit/fasta_formatter.xml delete mode 100644 tools/fastx_toolkit/fasta_nucleotide_changer.xml delete mode 100644 tools/fastx_toolkit/fastq_quality_boxplot.xml delete mode 100644 tools/fastx_toolkit/fastq_quality_converter.xml delete mode 100644 tools/fastx_toolkit/fastq_quality_filter.xml delete mode 100644 tools/fastx_toolkit/fastq_to_fasta.xml delete mode 100644 tools/fastx_toolkit/fastx_artifacts_filter.xml delete mode 100644 tools/fastx_toolkit/fastx_barcode_splitter.xml delete mode 100755 tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh delete mode 100644 tools/fastx_toolkit/fastx_clipper.xml delete mode 100644 tools/fastx_toolkit/fastx_collapser.xml delete mode 100644 tools/fastx_toolkit/fastx_nucleotides_distribution.xml delete mode 100644 tools/fastx_toolkit/fastx_quality_statistics.xml delete mode 100644 tools/fastx_toolkit/fastx_renamer.xml delete mode 100644 tools/fastx_toolkit/fastx_reverse_complement.xml delete mode 100644 tools/fastx_toolkit/fastx_trimmer.xml delete mode 100755 tools/phenotype_association/ctd.pl delete mode 100644 tools/phenotype_association/ctd.xml delete mode 100755 tools/phenotype_association/disease_ontology_gene_fuzzy_selector.pl delete mode 100755 tools/phenotype_association/dividePgSnpAlleles.pl delete mode 100644 tools/phenotype_association/dividePgSnpAlleles.xml delete mode 100644 tools/phenotype_association/funDo.xml delete mode 100755 tools/phenotype_association/hilbertvis.sh delete mode 100644 tools/phenotype_association/hilbertvis.xml delete mode 100755 tools/plotting/r_wrapper.sh delete mode 100644 tools/plotting/xy_plot.xml delete mode 100644 tools/regVariation/categorize_elements_satisfying_criteria.pl delete mode 100644 tools/regVariation/categorize_elements_satisfying_criteria.xml delete mode 100644 tools/regVariation/compute_motif_frequencies_for_all_motifs.pl delete mode 100644 tools/regVariation/compute_motif_frequencies_for_all_motifs.xml delete mode 100755 tools/regVariation/compute_motifs_frequency.pl delete mode 100755 tools/regVariation/compute_motifs_frequency.xml delete mode 100644 tools/regVariation/delete_overlapping_indels.pl delete mode 100644 tools/regVariation/delete_overlapping_indels.xml delete mode 100644 tools/regVariation/draw_stacked_barplots.pl delete mode 100644 tools/regVariation/draw_stacked_barplots.xml delete mode 100644 tools/regVariation/getIndels_3way.xml delete mode 100755 tools/regVariation/microsatellite_birthdeath.pl delete mode 100755 tools/regVariation/microsatellite_birthdeath.xml delete mode 100755 tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl delete mode 100755 tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml delete mode 100644 tools/regVariation/parseMAF_smallIndels.pl delete mode 100644 tools/regVariation/t_test_two_samples.pl delete mode 100644 tools/regVariation/t_test_two_samples.xml delete mode 100644 tools/samtools/bam_to_sam.py delete mode 100644 tools/samtools/bam_to_sam.xml delete mode 100644 tools/samtools/pileup_interval.py delete mode 100644 tools/samtools/pileup_interval.xml delete mode 100755 tools/samtools/pileup_parser.pl delete mode 100644 tools/samtools/pileup_parser.xml delete mode 100644 tools/samtools/sam2interval.py delete mode 100644 tools/samtools/sam2interval.xml delete mode 100755 tools/samtools/sam_bitwise_flag_filter.py delete mode 100644 tools/samtools/sam_bitwise_flag_filter.xml delete mode 100644 tools/samtools/sam_merge.py delete mode 100644 tools/samtools/sam_merge.xml delete mode 100644 tools/samtools/sam_merge_code.py delete mode 100644 tools/samtools/sam_pileup.py delete mode 100644 tools/samtools/sam_pileup.xml delete mode 100644 tools/samtools/sam_to_bam.py delete mode 100644 tools/samtools/sam_to_bam.xml delete mode 100644 tools/samtools/samtools_flagstat.xml delete mode 100644 tools/samtools/samtools_mpileup.xml delete mode 100644 tools/samtools/samtools_rmdup.xml delete mode 100644 tools/samtools/samtools_slice_bam.py delete mode 100644 tools/samtools/samtools_slice_bam.xml delete mode 100644 tools/samtools/samtools_wrapper.py diff --git a/lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py b/lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py new file mode 100644 index 00000000000..e028d455afa --- /dev/null +++ b/lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py @@ -0,0 +1,106 @@ +""" +The following tools have been eliminated from the distribution: + +1: BAM-to-SAM converts BAM format to SAM format +2: Categorize Elements satisfying criteria +3: Compute Motif Frequencies For All Motifs motif by motif +4: Compute Motif Frequencies in indel flanking regions +5: CTD analysis of chemicals, diseases, or genes +6: Delete Overlapping Indels from a chromosome indels file +7: Separate pgSnp alleles into columns +8: Draw Stacked Bar Plots for different categories and different criteria +9: Length Distribution chart +10: FASTA Width formatter +11: RNA/DNA converter +12: Draw quality score boxplot +13: Quality format converter (ASCII-Numeric) +14: Filter by quality +15: FASTQ to FASTA converter +16: Remove sequencing artifacts +17: Barcode Splitter +18: Clip adapter sequences +19: Collapse sequences +20: Draw nucleotides distribution chart +21: Compute quality statistics +22: Rename sequences +23: Reverse- Complement +24: Trim sequences +25: FunDO human genes associated with disease terms +26: HVIS visualization of genomic data with the Hilbert curve +27: Fetch Indels from 3-way alignments +28: Identify microsatellite births and deaths +29: Extract orthologous microsatellites for multiple (>2) species alignments +30: Mutate Codons with SNPs +31: Pileup-to-Interval condenses pileup format into ranges of bases +32: Filter pileup on coverage and SNPs +33: Filter SAM on bitwise flag values +34: Merge BAM Files merges BAM files together +35: Generate pileup from BAM dataset +36: SAM-to-BAM converts SAM format to BAM format +37: Convert SAM to interval +38: flagstat provides simple stats on BAM files +39: MPileup SNP and indel caller +40: rmdup remove PCR duplicates +41: Slice BAM by provided regions +42: Split paired end reads +43: T Test for Two Samples +44: Plotting tool for multiple series and graph types. + +The tools are now available in the repositories respectively: + +1: bam_to_sam +2: categorize_elements_satisfying_criteria +3: compute_motif_frequencies_for_all_motifs +4: compute_motifs_frequency +5: ctd_batch +6: delete_overlapping_indels +7: divide_pg_snp +8: draw_stacked_barplots +9: fasta_clipping_histogram +10: fasta_formatter +11: fasta_nucleotide_changer +12: fastq_quality_boxplot +13: fastq_quality_converter +14: fastq_quality_filter +15: fastq_to_fasta +16: fastx_artifacts_filter +17: fastx_barcode_splitter +18: fastx_clipper +19: fastx_collapser +20: fastx_nucleotides_distribution +21: fastx_quality_statistics +22: fastx_renamer +23: fastx_reverse_complement +24: fastx_trimmer +25: hgv_fundo +26: hgv_hilbertvis +27: indels_3way +28: microsatellite_birthdeath +29: multispecies_orthologous_microsats +30: mutate_snp_codon +31: pileup_interval +32: pileup_parser +33: sam_bitwise_flag_filter +34: sam_merge +35: sam_pileup +36: sam_to_bam +37: sam2interval +38: samtools_flagstat +39: samtools_mpileup +40: samtools_rmdup +41: samtools_slice_bam +42: split_paired_reads +43: t_test_two_samples +44: xy_plot + +from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu +and will be installed into your local Galaxy instance at the +location discussed above by running the following command. + +""" + +def upgrade( migrate_engine ): + print __doc__ + +def downgrade( migrate_engine ): + pass diff --git a/scripts/migrate_tools/0008_tools.sh b/scripts/migrate_tools/0008_tools.sh new file mode 100644 index 00000000000..50cafd19936 --- /dev/null +++ b/scripts/migrate_tools/0008_tools.sh @@ -0,0 +1,4 @@ +#!/bin/sh + +cd `dirname $0`/../.. +python ./scripts/migrate_tools/migrate_tools.py 0008_tools.xml $@ diff --git a/scripts/migrate_tools/0008_tools.xml b/scripts/migrate_tools/0008_tools.xml new file mode 100644 index 00000000000..339f1b3efbf --- /dev/null +++ b/scripts/migrate_tools/0008_tools.xml @@ -0,0 +1,135 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/test-data/1.bam 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CI -chrM 902 A 2 ,. II -chrM 903 A 2 ,. II -chrM 904 T 2 ,. II -chrM 905 C 3 ,.^:, III -chrM 906 A 3 ,., III -chrM 907 G 3 ,., III -chrM 908 G 3 ,., III -chrM 909 C 3 ,., III -chrM 910 C 3 ,., III -chrM 911 A 4 ,.,^:, IIII -chrM 912 T 4 ,.,, IIEG -chrM 913 G 4 ,.,, III: -chrM 914 A 4 ,.,, IIII -chrM 915 A 4 ,.,, IIII -chrM 916 G 4 ,.,, III5 -chrM 917 C 4 ,.,, III5 -chrM 918 G 4 ,.,, IIII -chrM 919 C 4 ,.,, III< -chrM 920 G 4 ,.,, IIII -chrM 921 C 4 ,.,, IIII -chrM 922 A 4 ,.,, IIII -chrM 923 C 4 ,.,, III8 -chrM 924 A 4 ,.,, IFII -chrM 925 C 4 ,.,, IIII -chrM 926 A 4 ,.,, IIII -chrM 927 C 4 ,.,, IIII -chrM 928 C 5 ,.,,^:, IIII: -chrM 929 G 5 ,.,,, IIIE: -chrM 930 C 5 ,.,,, IIIII -chrM 931 C 5 ,.,,, IIIIF -chrM 932 C 5 ,.,,, IIIIC -chrM 933 G 5 ,$.,,, I?II: -chrM 934 T 4 .$,,, 4II> -chrM 935 C 3 ,,, III -chrM 936 A 3 ,,, III -chrM 937 C 3 ,,, II1 -chrM 938 C 3 ,,, III -chrM 939 C 3 ,,, III -chrM 940 T 3 ,$,, III -chrM 941 C 2 ,, II -chrM 942 C 2 ,, I' -chrM 943 T 2 ,, II -chrM 944 T 2 ,, II -chrM 945 A 2 ,, II -chrM 946 A 2 ,$, II -chrM 947 A 1 , I -chrM 948 T 1 , I -chrM 949 A 1 , I -chrM 950 T 1 , I -chrM 951 C 1 , I -chrM 952 A 1 , I -chrM 953 C 1 , I -chrM 954 A 1 , I -chrM 955 A 2 ,^:. II -chrM 956 A 2 ,. II -chrM 957 T 2 ,. II -chrM 958 C 3 ,.^:. III -chrM 959 A 3 ,.. III -chrM 960 T 3 ,.. III -chrM 961 A 3 ,.. III -chrM 962 A 3 ,.. III -chrM 963 C 4 ,$..^:. IIII -chrM 964 A 3 ... I(; -chrM 965 T 3 ... III -chrM 966 A 4 ...^:. IIII -chrM 967 A 4 .... IIII -chrM 968 C 4 .... IEII -chrM 969 A 4 .... IIII -chrM 970 T 4 .... IIII -chrM 971 A 4 .... IIII -chrM 972 A 4 .... IIII -chrM 973 A 4 .... II0I -chrM 974 A 5 ....^:. IIIII -chrM 975 C 5 ..... IIIII -chrM 976 C 5 ..... IIIII -chrM 977 G 5 ..... IIIII -chrM 978 T 5 ..... IIIII -chrM 979 G 5 ..... I0III -chrM 980 A 5 ..... IIII4 -chrM 981 C 5 ..... IIIII -chrM 982 C 5 ..... IIIII -chrM 983 C 5 ..... IIIII -chrM 984 A 5 ..... -IGII -chrM 985 A 5 ..... 4GIII -chrM 986 A 5 ..... BDGII -chrM 987 C 5 ..... IDIII -chrM 988 A 5 ..... @ + -
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