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Source code for galaxy.tool_shed.galaxy_install.migrate.versions.0009_tools
""" 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. """[docs]def upgrade(migrate_engine): print(__doc__)[docs]def downgrade(migrate_engine): pass