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tool_shed.galaxy_install.migrate.versions package¶
Submodules¶
tool_shed.galaxy_install.migrate.versions.0001_tools module¶
Initialize the version column of the migrate_tools database table to 1. No tool migrations are handled in this version.
tool_shed.galaxy_install.migrate.versions.0002_tools module¶
The Emboss 5.0.0 tools have been eliminated from the distribution and the Emboss datatypes have been removed from datatypes_conf.xml.sample. You should remove the Emboss datatypes from your version of datatypes_conf.xml. The repositories named emboss_5 and emboss_datatypes from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu will be installed into your local Galaxy instance at the location discussed above by running the following command.
tool_shed.galaxy_install.migrate.versions.0003_tools module¶
The freebayes tool has been eliminated from the distribution . The repository named freebayes from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu will be installed into your local Galaxy instance at the location discussed above by running the following command.
tool_shed.galaxy_install.migrate.versions.0004_tools module¶
The NCBI BLAST+ tools have been eliminated from the distribution. The tools and datatypes are now available in repositories named ncbi_blast_plus and blast_datatypes, in the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu. These repositories will be installed into your local Galaxy instance at the location discussed above by running the following command.
tool_shed.galaxy_install.migrate.versions.0005_tools module¶
The tools “Map with BWA for Illumina” and “Map with BWA for SOLiD” have been eliminated from the distribution. The tools are now available in the repository named bwa_wrappers 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.
tool_shed.galaxy_install.migrate.versions.0006_tools module¶
The following tools have been eliminated from the distribution: FASTQ to BAM, SAM to FASTQ, BAM Index Statistics, Estimate Library Complexity, Insertion size metrics for PAIRED data, SAM/BAM Hybrid Selection Metrics, bam/sam Cleaning, Add or Replace Groups, Replace SAM/BAM Header, Paired Read Mate Fixer, Mark Duplicate reads, SAM/BAM Alignment Summary Metrics, SAM/BAM GC Bias Metrics, and Reorder SAM/BAM. The tools are now available in the repository named picard 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.
tool_shed.galaxy_install.migrate.versions.0007_tools module¶
The following tools have been eliminated from the distribution: Map with Bowtie for Illumina, Map with Bowtie for SOLiD, Lastz, and Lastz paired reads. The tools are now available in the repositories named bowtie_wrappers, bowtie_color_wrappers, lastz, and lastz_paired_reads 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.
tool_shed.galaxy_install.migrate.versions.0008_tools module¶
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: Cuffcompare 7: Cuffdiff 8: Cufflinks 9: Cuffmerge 10: Delete Overlapping Indels from a chromosome indels file 11: Separate pgSnp alleles into columns 12: Draw Stacked Bar Plots for different categories and different criteria 13: Length Distribution chart 14: FASTA Width formatter 15: RNA/DNA converter 16: Draw quality score boxplot 17: Quality format converter (ASCII-Numeric) 18: Filter by quality 19: FASTQ to FASTA converter 20: Remove sequencing artifacts 21: Barcode Splitter 22: Clip adapter sequences 23: Collapse sequences 24: Draw nucleotides distribution chart 25: Compute quality statistics 26: Rename sequences 27: Reverse- Complement 28: Trim sequences 29: FunDO human genes associated with disease terms 30: HVIS visualization of genomic data with the Hilbert curve 31: Fetch Indels from 3-way alignments 32: Identify microsatellite births and deaths 33: Extract orthologous microsatellites for multiple (>2) species alignments 34: Mutate Codons with SNPs 35: Pileup-to-Interval condenses pileup format into ranges of bases 36: Filter pileup on coverage and SNPs 37: Filter SAM on bitwise flag values 38: Merge BAM Files merges BAM files together 39: Generate pileup from BAM dataset 40: SAM-to-BAM converts SAM format to BAM format 41: Convert SAM to interval 42: flagstat provides simple stats on BAM files 43: MPileup SNP and indel caller 44: rmdup remove PCR duplicates 45: Slice BAM by provided regions 46: Split paired end reads 47: T Test for Two Samples 48: 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: cuffcompare 7: cuffdiff 8: cufflinks 9: cuffmerge 10: delete_overlapping_indels 11: divide_pg_snp 12: draw_stacked_barplots 13: fasta_clipping_histogram 14: fasta_formatter 15: fasta_nucleotide_changer 16: fastq_quality_boxplot 17: fastq_quality_converter 18: fastq_quality_filter 19: fastq_to_fasta 20: fastx_artifacts_filter 21: fastx_barcode_splitter 22: fastx_clipper 23: fastx_collapser 24: fastx_nucleotides_distribution 25: fastx_quality_statistics 26: fastx_renamer 27: fastx_reverse_complement 28: fastx_trimmer 29: hgv_fundo 30: hgv_hilbertvis 31: indels_3way 32: microsatellite_birthdeath 33: multispecies_orthologous_microsats 34: mutate_snp_codon 35: pileup_interval 36: pileup_parser 37: sam_bitwise_flag_filter 38: sam_merge 39: sam_pileup 40: sam_to_bam 41: sam2interval 42: samtools_flagstat 43: samtools_mpileup 44: samtools_rmdup 45: samtools_slice_bam 46: split_paired_reads 47: t_test_two_samples 48: 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.
tool_shed.galaxy_install.migrate.versions.0009_tools module¶
The following tools have been eliminated from the distribution:
1: Bowtie2 2: Control-based ChIP-seq Analysis Tool 3: ClustalW multiple sequence alignment program for DNA or proteins 4: Compute P-values and Correlation Coefficients for Feature Occurrences 5: Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features 6: Compute P-values and Second Moments for Feature Occurrences 7: Compute P-values and Max Variances for Feature Occurrences 8: Wavelet variance using Discrete Wavelet Transfoms 9: Quantify the abundances of a set of target sequences from sampled subsequences 10: Read QC reports using FastQC 11: Combine FASTA and QUAL into FASTQ. 12: Filter FASTQ reads by quality score and length 13: Convert between various FASTQ quality formats. 14: Manipulate FASTQ reads on various attributes. 15: FASTQ Masker by quality score 16: FASTQ de-interlacer on paired end reads. 17: FASTQ interlacer on paired end reads 18: FASTQ joiner on paired end reads 19: FASTQ splitter on joined paired end reads 20: FASTQ Summary Statistics by column 21: FASTQ to FASTA converter 22: FASTQ to Tabular converter 23: FASTQ Trimmer by quality 24: FASTQ Quality Trimmer by sliding window 25: Filter Combined Transcripts 26: find_diag_hits 27: Call SNPS with Freebayes 28: Fetch taxonomic representation 29: GMAJ Multiple Alignment Viewer 30: Find lowest diagnostic rank 31: Model-based Analysis of ChIP-Seq 32: Poisson two-sample test 33: Statistical approach for the Identification of ChIP-Enriched Regions 34: Draw phylogeny 35: Summarize taxonomy 36: Tabular to FASTQ converter 37: Find splice junctions using RNA-seq data 38: Gapped-read mapper for RNA-seq data 39: Annotate a VCF file (dbSNP, hapmap) 40: Extract reads from a specified region 41: Filter a VCF file 42: Generate the intersection of two VCF files 43: Sequence Logo generator for fasta (eg Clustal alignments)
The tools are now available in the repositories respectively:
1: bowtie2 2: ccat 3: clustalw 4: dwt_cor_ava_perclass 5: dwt_cor_avb_all 6: dwt_ivc_all 7: dwt_var_perclass 8: dwt_var_perfeature 9: express 10: fastqc 11: fastq_combiner 12: fastq_filter 13: fastq_groomer 14: fastq_manipulation 15: fastq_masker_by_quality 16: fastq_paired_end_deinterlacer 17: fastq_paired_end_interlacer 18: fastq_paired_end_joiner 19: fastq_paired_end_splitter 20: fastq_stats 21: fastqtofasta 22: fastq_to_tabular 23: fastq_trimmer 24: fastq_trimmer_by_quality 25: filter_transcripts_via_tracking 26: find_diag_hits 27: freebayes_wrapper 28: gi2taxonomy 29: gmaj 30: lca_wrapper 31: macs 32: poisson2test 33: sicer 34: t2ps 35: t2t_report 36: tabular_to_fastq 37: tophat 38: tophat2 39: vcf_annotate 40: vcf_extract 41: vcf_filter 42: vcf_intersect 43: weblogo3
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.
tool_shed.galaxy_install.migrate.versions.0010_tools module¶
The following tools have been eliminated from the distribution:
- Analyze Covariates
- Base Coverage of all intervals
- Perform Best-subsets Regression
- Cluster
- Complement intervals of a dataset
- Compute q-values based on multiple simultaneous tests p-values
- Concatenate two datasets into one dataset
- Count Covariates on BAM files
- Coverage of a set of intervals on second set of intervals
- Depth of Coverage on BAM files
- Feature coverage
- Fetch closest non-overlapping feature for every interval
- Get flanks - returns flanking region/s for every gene
- Estimate Indel Rates for 3-way alignments
- Fetch Indels from pairwise alignments
- Indel Realigner - perform local realignment
- Intersect the intervals of two datasets
- Join the intervals of two datasets side-by-side
- Perform Linear Regression
- Perform Logistic Regression with vif
- Mask CpG/non-CpG sites from MAF file
- Merge the overlapping intervals of a dataset
- Extract Orthologous Microsatellites from pair-wise alignments
- Estimate microsatellite mutability by specified attributes
- Compute partial R square
- Print Reads from BAM files
- Filter nucleotides based on quality scores
- Compute RCVE
- Realigner Target Creator for use in local realignment
- Estimate substitution rates for non-coding regions
- Fetch substitutions from pairwise alignments
- Subtract the intervals of two datasets
- Subtract Whole Dataset from another dataset
- Table Recalibration on BAM files
- Arithmetic Operations on tables
- Unified Genotyper SNP and indel caller
- Variant Annotator
- Apply Variant Recalibration
- Combine Variants
- Eval Variants
- Variant Filtration on VCF files
- Variant Recalibrator
- Select Variants from VCF files
- Validate Variants
- Assign weighted-average of the values of features overlapping an interval
- Make windows
The tools are now available in the repositories respectively:
- analyze_covariates
- basecoverage
- best_regression_subsets
- cluster
- complement
- compute_q_values
- concat
- count_covariates
- coverage
- depth_of_coverage
- featurecounter
- flanking_features
- get_flanks
- getindelrates_3way
- getindels_2way
- indel_realigner
- intersect
- join
- linear_regression
- logistic_regression_vif
- maf_cpg_filter
- merge
- microsats_alignment_level
- microsats_mutability
- partialr_square
- print_reads
- quality_filter
- rcve
- realigner_target_creator
- substitution_rates
- substitutions
- subtract
- subtract_query
- table_recalibration
- tables_arithmetic_operations
- unified_genotyper
- variant_annotator
- variant_apply_recalibration
- variant_combine
- variant_eval
- variant_filtration
- variant_recalibrator
- variant_select
- variants_validate
- weightedaverage
- windowsplitter
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.
tool_shed.galaxy_install.migrate.versions.0011_tools module¶
The following tools have been eliminated from the distribution:
1: Profile Annotations for a set of genomic intervals 2: Polymorphism of the Reads 3: Coverage of the Reads in wiggle format 4: Canonical Correlation Analysis 5: Convert Color Space to Nucleotides 6: Compute sequence length 7: Concatenate FASTA alignment by species 8: Filter sequences by length 9: FASTA-to-Tabular converter 10: FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data 11: Kernel Canonical Correlation Analysis 12: Kernel Principal Component Analysis 13: Format mapping data as UCSC custom track 14: Megablast compare short reads against htgs, nt, and wgs databases 15: Parse blast XML output 16: Principal Component Analysis 17: RMAP for Solexa Short Reads Alignment 18: RMAPQ for Solexa Short Reads Alignment with Quality Scores 19: Histogram of high quality score reads 20: Build base quality distribution 21: Select high quality segments 22: Tabular-to-FASTA
The tools are now available in the repositories respectively:
1: annotation_profiler 2: blat_coverage_report 3: blat_mapping 4: canonical_correlation_analysis 5: convert_solid_color2nuc 6: fasta_compute_length 7: fasta_concatenate_by_species 8: fasta_filter_by_length 9: fasta_to_tabular 10: fastqsolexa_to_fasta_qual 11: kernel_canonical_correlation_analysis 12: kernel_principal_component_analysis 13: mapping_to_ucsc 14: megablast_wrapper 15: megablast_xml_parser 16: principal_component_analysis 17: rmap 18: rmapq 19: short_reads_figure_high_quality_length 20: short_reads_figure_score 21: short_reads_trim_seq 22: tabular_to_fasta
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.
tool_shed.galaxy_install.migrate.versions.0012_tools module¶
The following tools have been eliminated from the distribution:
1: Compute an expression on every row 2: Correlation for numeric columns 3: Count GFF Features 4: Filter on ambiguities in polymorphism datasets 5: Generate A Matrix for using PC and LDA 6: Histogram of a numeric column 7: Perform Linear Discriminant Analysis 8: Maximal Information-based Nonparametric Exploration 9: Pearson and apos Correlation between any two numeric columns 10: Convert from pgSnp to gd_snp 11: Draw ROC plot on "Perform LDA" output 12: Scatterplot of two numeric columns 13: snpFreq significant SNPs in case-control data 14: Build custom track for UCSC genome browser 15: VCF to pgSnp
The tools are now available in the repositories respectively:
1: column_maker 2: correlation 3: count_gff_features 4: dna_filtering 5: generate_pc_lda_matrix 6: histogram 7: lda_analysis 8: mine 9: pearson_correlation 10: pgsnp2gd_snp 11: plot_from_lda 12: scatterplot 13: snpfreq 14: ucsc_custom_track 15: vcf2pgsnp
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.