From 113d50f2a2394c805484d0eac4c48e6c53f1d1fe Mon Sep 17 00:00:00 2001 From: Johan Gustafsson Date: Fri, 30 Aug 2024 14:28:11 +0930 Subject: [PATCH] Content update --- data/data.yaml | 482 +++++++++++++++++++++++++++++++++++++++++-------- 1 file changed, 406 insertions(+), 76 deletions(-) diff --git a/data/data.yaml b/data/data.yaml index 12971ad..aad9048 100644 --- a/data/data.yaml +++ b/data/data.yaml @@ -674,6 +674,13 @@ - Data management - Sequence analysis galaxy: + - description: 'Operate on and transform BAM: datasets in various ways' + title: Operate on and transform BAM 2.5.2+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fbamtools%2Fbamtools%2F2.5.2%2Bgalaxy2 + - description: 'Split BAM by reads mapping status: into a mapped and an unmapped + dataset' + title: Split BAM by reads mapping status 2.5.2+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbamtools_split_mapped%2Fbamtools_split_mapped%2F2.5.2%2Bgalaxy2 - description: 'Split BAM by read tag value: into a dataset list collection' title: Split BAM by read tag value 2.5.2+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fbamtools_split_tag%2Fbamtools_split_tag%2F2.5.2%2Bgalaxy2 @@ -3435,6 +3442,45 @@ resources: - title: .nan url: .nan +- biocontainers: '' + biotools: chira + bunya: '' + description: ChiRA is a tool suite to analyze RNA-RNA interactome experimental data + such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. + edam-inputs: '' + edam-operations: '' + edam-outputs: '' + edam-topics: + - RNA + - Molecular interactions, pathways and networks + - Functional, regulatory and non-coding RNA + galaxy: + - description: 'ChiRA qauntify: quantify aligned loci to score the alignments' + title: ChiRA qauntify 1.4.30 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fchira_quantify%2Fchira_quantify%2F1.4.30 + - description: 'ChiRA merge: merge aligned positions' + title: ChiRA merge 1.4.30 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fchira_merge%2Fchira_merge%2F1.4.30 + - description: 'ChiRA extract: extrat the chimeras' + title: ChiRA extract 1.4.31 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fchira_extract%2Fchira_extract%2F1.4.31 + - description: 'ChiRA collapse: deduplicate fastq reads' + title: ChiRA collapse 1.4.31 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fchira_collapse%2Fchira_collapse%2F1.4.31 + - description: 'ChiRA map: map reads to trascriptome' + title: ChiRA map 1.4.30 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fchira_map%2Fchira_map%2F1.4.30 + homepage: https://github.com/pavanvidem/chira + id: chira + license: GPL-3.0 + name: ChiRA + nci-gadi: '' + nci-if89: '' + pawsey: '' + publications: '' + resources: + - title: .nan + url: .nan - biocontainers: '' biotools: chromeister bunya: '' @@ -7190,6 +7236,9 @@ edam-outputs: '' edam-topics: '' galaxy: + - description: 'Split by group: ' + title: Split by group 0.6 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fsplit_file_on_column%2Ftp_split_on_column%2F0.6 - description: 'Split file: to dataset collection' title: Split file 0.5.2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fsplit_file_to_collection%2Fsplit_file_to_collection%2F0.5.2 @@ -7308,145 +7357,151 @@ - description: 'LAV to BED: Converts a LAV formatted file to BED format' title: LAV to BED 1.0.0 url: https://usegalaxy.org.au/root?tool_id=lav_to_bed1 - - description: 'Convert Genomic Intervals To Strict BED: ' - title: Convert Genomic Intervals To Strict BED 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bedstrict_0 - - description: 'OpenBabel converter for molecular formats: ' - title: OpenBabel converter for molecular formats 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_molecules + - description: 'Convert SAM to BAM without sorting: ' + title: Convert SAM to BAM without sorting 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_unsorted_bam - description: 'Convert FASTQ files to seek locations: ' title: Convert FASTQ files to seek locations 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fastq_to_fqtoc0 - description: 'Convert Wiggle to BigWig: ' title: Convert Wiggle to BigWig 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wig_to_bigwig - - description: 'Convert BAM to BigWig: ' - title: Convert BAM to BigWig 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_bigwig_0 + - description: 'Convert GRO to PDB: ' + title: Convert GRO to PDB 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Gro_to_Pdb_0 - description: 'Convert uncompressed file to compressed: ' title: Convert uncompressed file to compressed 1.16+galaxy0 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_uncompressed_to_gz - - description: 'Convert MOL2 to MOL: ' - title: Convert MOL2 to MOL 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mol2_to_mol - - description: 'Convert Picard Interval List to BED6: converter' - title: Convert Picard Interval List to BED6 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_picard_interval_list_to_bed6 - description: 'Convert Interval to BGZIP: ' title: Convert Interval to BGZIP 1.0.3 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bgzip_0 + - description: 'Convert BAM to coordinate-sorted BAM: ' + title: Convert BAM to coordinate-sorted BAM 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_coodinate_sorted_bam + - description: 'Convert BAM to BigWig: ' + title: Convert BAM to BigWig 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_bigwig_0 + - description: 'OpenBabel converter for molecular formats: ' + title: OpenBabel converter for molecular formats 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_molecules + - description: 'Convert Picard Interval List to BED6: converter' + title: Convert Picard Interval List to BED6 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_picard_interval_list_to_bed6 - description: 'Convert tabular to CSV: ' title: Convert tabular to CSV 1.0.0 url: https://usegalaxy.org.au/root?tool_id=tabular_to_csv - - description: 'Convert Genomic Intervals To Strict BED12: ' - title: Convert Genomic Intervals To Strict BED12 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed12_0 - description: 'Convert compressed file to uncompressed.: ' title: Convert compressed file to uncompressed. 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bz2_to_uncompressed - - description: 'Convert GRO to PDB: ' - title: Convert GRO to PDB 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Gro_to_Pdb_0 + - description: 'Convert Genomic Intervals To Strict BED12: ' + title: Convert Genomic Intervals To Strict BED12 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed12_0 - description: 'Convert MAF to Genomic Intervals: ' title: Convert MAF to Genomic Intervals 1.0.3 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_interval_0 + - description: 'Convert XTC, DCD, and TRR: ' + title: Convert XTC, DCD, and TRR 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mdconvert - description: 'Convert lped to plink pbed: ' title: Convert lped to plink pbed 0.02 url: https://usegalaxy.org.au/root?tool_id=lped2pbedconvert - description: 'Convert BED, GFF, or VCF to BigWig: ' title: Convert BED, GFF, or VCF to BigWig 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bed_gff_or_vcf_to_bigwig_0 - - description: 'Convert FASTA to Tabular: ' - title: Convert FASTA to Tabular 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_tabular + - description: 'Convert CML to SMILES: ' + title: Convert CML to SMILES 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cml_to_smiles - description: 'Convert compressed file to uncompressed.: ' title: Convert compressed file to uncompressed. 1.0.0 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gz_to_uncompressed + - description: 'Convert FASTA to Tabular: ' + title: Convert FASTA to Tabular 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_tabular + - description: 'Convert Interval to tabix: ' + title: Convert Interval to tabix 1.0.2 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_tabix_0 - description: 'Convert Len file to Linecount: ' title: Convert Len file to Linecount 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_len_to_linecount - - description: 'Convert BAM to coordinate-sorted BAM: ' - title: Convert BAM to coordinate-sorted BAM 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_coodinate_sorted_bam + - description: 'Convert MOL2 to MOL: ' + title: Convert MOL2 to MOL 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mol2_to_mol - description: 'Convert SMILES to MOL: ' title: Convert SMILES to MOL 2.4.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_SMILES_to_MOL - - description: 'Convert XTC, DCD, and TRR: ' - title: Convert XTC, DCD, and TRR 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_mdconvert - description: 'Convert GFF to Interval Index: ' title: Convert GFF to Interval Index 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_interval_index_0 + - description: 'Convert InChI to MOL: ' + title: Convert InChI to MOL 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_inchi_to_mol - description: 'Convert BigWig to Wiggle: Convert bigWig to wig' title: Convert BigWig to Wiggle 377+galaxy0 url: https://usegalaxy.org.au/root?tool_id=bigwigtowig - - description: 'Convert CML to SMILES: ' - title: Convert CML to SMILES 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cml_to_smiles - description: 'Convert compressed and uncompressed BCF files: ' title: Convert compressed and uncompressed BCF files 0.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bcf_uncompressed_to_bcf + - description: 'Convert Ref taxonomy to Seq Taxonomy: converts 2 or 3 column sequence + taxonomy file to a 2 column mothur taxonomy_outline format' + title: Convert Ref taxonomy to Seq Taxonomy 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_ref_to_seq_taxomony - description: 'Convert tar to directory: ' title: Convert tar to directory 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_tar_to_directory - - description: 'Convert InChI to MOL: ' - title: Convert InChI to MOL 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_inchi_to_mol - description: 'Convert Genomic Intervals To BED: ' title: Convert Genomic Intervals To BED 1.0.0 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed_0 - - description: 'Convert Ref taxonomy to Seq Taxonomy: converts 2 or 3 column sequence - taxonomy file to a 2 column mothur taxonomy_outline format' - title: Convert Ref taxonomy to Seq Taxonomy 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_ref_to_seq_taxomony - - description: 'SMILES to SMILES: ' - title: SMILES to SMILES 2.4.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_smiles_to_smiles + - description: 'Convert SAM to BigWig: ' + title: Convert SAM to BigWig 1.0.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_bigwig_0 - description: 'Convert BAM to queryname-sorted BAM: ' title: Convert BAM to queryname-sorted BAM 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bam_to_qname_sorted_bam - description: 'Convert FASTA to Bowtie base space Index: ' title: Convert FASTA to Bowtie base space Index 1.3.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_base_index - - description: 'Convert Interval to tabix: ' - title: Convert Interval to tabix 1.0.2 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_tabix_0 - - description: 'Convert FASTA to fai file: ' - title: Convert FASTA to fai file 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_fai - description: 'Convert plink pbed to ld reduced format: ' title: Convert plink pbed to ld reduced format 0.02 url: https://usegalaxy.org.au/root?tool_id=pbed2ldindepconvert + - description: 'Convert FASTA to fai file: ' + title: Convert FASTA to fai file 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_fai - description: 'Convert BGZ VCF to tabix: ' title: Convert BGZ VCF to tabix 1.0.2 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_vcf_bgzip_to_tabix_0 - - description: 'Convert plink pbed to linkage lped: ' - title: Convert plink pbed to linkage lped 0.02 - url: https://usegalaxy.org.au/root?tool_id=pbed2lpedconvert - description: 'Convert neostore.zip files to neostore: ' title: Convert neostore.zip files to neostore 1.0.0 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_neostorezip_to_neostore - - description: 'Convert Genomic Intervals To Strict BED6: ' - title: Convert Genomic Intervals To Strict BED6 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed6_0 + - description: 'Convert plink pbed to linkage lped: ' + title: Convert plink pbed to linkage lped 0.02 + url: https://usegalaxy.org.au/root?tool_id=pbed2lpedconvert + - description: 'Convert BedGraph to BigWig: ' + title: Convert BedGraph to BigWig 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bedgraph_to_bigwig + - description: 'SMILES to SMILES: ' + title: SMILES to SMILES 2.4.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_smiles_to_smiles - description: 'Convert Wiggle to Interval: ' title: Convert Wiggle to Interval 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_wiggle_to_interval_0 - - description: 'Convert PDB to GRO: ' - title: Convert PDB to GRO 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Pdb_to_Gro_0 - - description: 'Convert FASTA to Bowtie color space Index: ' - title: Convert FASTA to Bowtie color space Index 1.2.3 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_color_index - description: 'Convert MAF to Fasta: ' title: Convert MAF to Fasta 1.0.2 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_maf_to_fasta_0 + - description: 'Convert FASTA to Bowtie color space Index: ' + title: Convert FASTA to Bowtie color space Index 1.2.3 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_bowtie_color_index + - description: 'Convert Genomic Intervals To Strict BED6: ' + title: Convert Genomic Intervals To Strict BED6 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bed6_0 + - description: 'Convert Genomic Intervals To Coverage: ' + title: Convert Genomic Intervals To Coverage 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bigwig_0 - description: 'Convert GFF to Feature Location Index: ' title: Convert GFF to Feature Location Index 1.0.0 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_gff_to_fli_0 - - description: 'Convert SAM to BigWig: ' - title: Convert SAM to BigWig 1.0.3 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_bigwig_0 + - description: 'Convert PDB to GRO: ' + title: Convert PDB to GRO 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Pdb_to_Gro_0 - description: 'Convert CRAM to BAM: ' title: Convert CRAM to BAM 1.0.2 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_cram_to_bam_0 @@ -7459,15 +7514,12 @@ - description: 'Convert Biom datasets: ' title: Convert Biom datasets 2.1.5 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_biom - - description: 'Convert CSV to tabular: ' - title: Convert CSV to tabular 1.0.0 - url: https://usegalaxy.org.au/root?tool_id=csv_to_tabular - description: 'Convert Bam to Bai: ' title: Convert Bam to Bai 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_Bam_Bai_0 - - description: 'Convert Genomic Intervals To Coverage: ' - title: Convert Genomic Intervals To Coverage 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bigwig_0 + - description: 'Convert CSV to tabular: ' + title: Convert CSV to tabular 1.0.0 + url: https://usegalaxy.org.au/root?tool_id=csv_to_tabular - description: 'Convert tabular to dbnsfp: ' title: Convert tabular to dbnsfp 1.0.2 url: https://usegalaxy.org.au/root?tool_id=tabular_to_dbnsfp @@ -7486,12 +7538,9 @@ - description: 'Convert FASTA to len file: ' title: Convert FASTA to len file 1.0.1 url: https://usegalaxy.org.au/root?tool_id=CONVERTER_fasta_to_len - - description: 'Convert BedGraph to BigWig: ' - title: Convert BedGraph to BigWig 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_bedgraph_to_bigwig - - description: 'Convert SAM to BAM without sorting: ' - title: Convert SAM to BAM without sorting 1.0.1 - url: https://usegalaxy.org.au/root?tool_id=CONVERTER_sam_to_unsorted_bam + - description: 'Convert Genomic Intervals To Strict BED: ' + title: Convert Genomic Intervals To Strict BED 1.0.1 + url: https://usegalaxy.org.au/root?tool_id=CONVERTER_interval_to_bedstrict_0 homepage: '' id: Galaxy CONVERTER license: '' @@ -7512,6 +7561,9 @@ edam-outputs: '' edam-topics: '' galaxy: + - description: 'EGA Download Client: ' + title: EGA Download Client 5.0.2+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fega_download_client%2Fpyega3%2F5.0.2%2Bgalaxy0 - description: 'UCSC Main: table browser' title: UCSC Main 1.0.0 url: https://usegalaxy.org.au//tool_runner/data_source_redirect?tool_id=ucsc_table_direct1 @@ -7786,6 +7838,9 @@ edam-outputs: '' edam-topics: '' galaxy: + - description: 'Add input name as column: to an existing tabular file' + title: Add input name as column 0.2.0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fmvdbeek%2Fadd_input_name_as_column%2FaddName%2F0.2.0 - description: 'SQLite to tabular: for SQL query' title: SQLite to tabular 3.2.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsqlite_to_tabular%2Fsqlite_to_tabular%2F3.2.1 @@ -9458,6 +9513,36 @@ resources: - title: .nan url: .nan +- biocontainers: '' + biotools: helixer + bunya: '' + description: Deep Learning to predict gene annotations + edam-inputs: [] + edam-operations: + - Gene prediction + - Genome annotation + edam-outputs: [] + edam-topics: + - Sequence analysis + - Gene transcripts + galaxy: + - description: 'Helixer: gene calling' + title: Helixer 0.3.2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fgenouest%2Fhelixer%2Fhelixer%2F0.3.2 + homepage: https://github.com/weberlab-hhu/Helixer + id: helixer + license: GPL-3.0 + name: Helixer + nci-gadi: '' + nci-if89: '' + pawsey: '' + publications: + - title: 'Helixer: Cross-species gene annotation of large eukaryotic genomes using + deep learning' + url: https://doi.org/10.1093/bioinformatics/btaa1044 + resources: + - title: .nan + url: .nan - biocontainers: '' biotools: hgv_david bunya: '' @@ -9786,6 +9871,10 @@ cluster consensus matrices' title: scHicPlotConsensusMatrices 4.1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fschicexplorer_schicplotconsensusmatrices%2Fschicexplorer_schicplotconsensusmatrices%2F4.1 + - description: 'hicPlotTADs: plot Hi-C contact matrices heatmaps alongside other + data tracks' + title: hicPlotTADs 2.1.4.0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicplottads%2Fhicexplorer_hicplottads%2F2.1.4.0 - description: 'hicPlotMatrix: plot a Hi-C contact matrix heatmap' title: hicPlotMatrix 3.7.5+galaxy0 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Fhicexplorer_hicplotmatrix%2Fhicexplorer_hicplotmatrix%2F3.7.5%2Bgalaxy0 @@ -12824,6 +12913,10 @@ - Ecology - Sequence assembly galaxy: + - description: 'megahit contig2fastg: for converting MEGAHIT''s contigs (.fa) to + assembly graphs (.fastg)' + title: megahit contig2fastg 1.1.3+galaxy1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmegahit_contig2fastg%2Fmegahit_contig2fastg%2F1.1.3%2Bgalaxy1 - description: 'MEGAHIT: for metagenomics assembly' title: MEGAHIT 1.2.9+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fmegahit%2Fmegahit%2F1.2.9%2Bgalaxy1 @@ -15919,6 +16012,29 @@ resources: - title: .nan url: .nan +- biocontainers: '' + biotools: '' + bunya: '' + description: '' + edam-inputs: '' + edam-operations: '' + edam-outputs: '' + edam-topics: '' + galaxy: + - description: 'Nucleotide subsequence search: providing regions in BED format' + title: Nucleotide subsequence search 0.2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ffind_subsequences%2Fbg_find_subsequences%2F0.2 + homepage: '' + id: bg_find_subsequences + license: '' + name: Nucleotide subsequence search + nci-gadi: '' + nci-if89: '' + pawsey: '' + publications: '' + resources: + - title: .nan + url: .nan - biocontainers: obitools biotools: obitools bunya: '' @@ -17480,6 +17596,40 @@ resources: - title: .nan url: .nan +- biocontainers: '' + biotools: PlasmidFinder + bunya: '' + description: PlasmidFinder is a tool for the identification and typing of Plasmid + Replicons in Whole-Genome Sequencing (WGS). + edam-inputs: [] + edam-operations: + - Genome assembly + - Scaffolding + - Multilocus sequence typing + edam-outputs: [] + edam-topics: + - Whole genome sequencing + - Sequence assembly + - Mapping + - Probes and primers + galaxy: + - description: 'PlasmidFinder: Plasmid identification in bacteria.' + title: PlasmidFinder 2.1.6+galaxy1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fplasmidfinder%2Fplasmidfinder%2F2.1.6%2Bgalaxy1 + homepage: https://cge.cbs.dtu.dk/services/PlasmidFinder/ + id: plasmidfinder + license: '' + name: PlasmidFinder + nci-gadi: '' + nci-if89: '' + pawsey: '' + publications: + - title: 'PlasmidFinder and In Silico pMLST: Identification and Typing of Plasmid + Replicons in Whole-Genome Sequencing (WGS)' + url: https://doi.org/10.1007/978-1-4939-9877-7_20 + resources: + - title: .nan + url: .nan - biocontainers: plink biotools: plink bunya: @@ -18996,6 +19146,89 @@ resources: - title: .nan url: .nan +- biocontainers: '' + biotools: ragtag + bunya: '' + description: RagTag is a collection of software tools for scaffolding and improving + modern genome assemblies. + edam-inputs: [] + edam-operations: + - Genome assembly + edam-outputs: [] + edam-topics: + - Sequence assembly + galaxy: + - description: 'RagTag: reference-guided scaffolding of draft genomes' + title: RagTag 2.1.0+galaxy1 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fragtag%2Fragtag%2F2.1.0%2Bgalaxy1 + homepage: https://github.com/malonge/RagTag + id: ragtag + license: MIT + name: ragtag + nci-gadi: '' + nci-if89: '' + pawsey: '' + publications: + - title: 'RaGOO: Fast and accurate reference-guided scaffolding of draft genomes' + url: https://doi.org/10.1186/s13059-019-1829-6 + resources: + - title: .nan + url: .nan +- biocontainers: '' + biotools: RaGOO + bunya: '' + description: 'fast and accurate reference-guided scaffolding of draft genomes. + + + Fast Reference-Guided Scaffolding of Genome Assembly Contigs. + + + Index of /shares/schatzlab/www-data/ragoo. + + + A tool to order and orient genome assembly contigs via Minimap2 alignments to + a reference genome. + + + Alonge, Michael, et al. "RaGOO: fast and accurate reference-guided scaffolding + of draft genomes." Genome biology 20.1 (2019): 1-17. + + + Contigs and reference fasta files may now be gzipped. + + + RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes + via minimap2 alignments to a closely related reference genome. The focus of this + tool is on practicality and therefore has the following features:' + edam-inputs: [] + edam-operations: + - Genome assembly + - Sequence trimming + - Scaffolding + - Genome alignment + edam-outputs: [] + edam-topics: + - Sequence assembly + - Sequencing + - Plant biology + - Cell biology + galaxy: + - description: 'RaGOO: Order and assign scaffolds' + title: RaGOO 1.0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdereeper%2Fragoo%2Fragoo%2F1.0 + homepage: https://github.com/malonge/RaGOO + id: ragoo + license: MIT + name: RaGOO + nci-gadi: '' + nci-if89: '' + pawsey: '' + publications: + - title: 'RaGOO: Fast and accurate reference-guided scaffolding of draft genomes' + url: https://doi.org/10.1186/S13059-019-1829-6 + resources: + - title: .nan + url: .nan - biocontainers: '' biotools: ramclustr bunya: '' @@ -19666,6 +19899,37 @@ resources: - title: .nan url: .nan +- biocontainers: '' + biotools: rnaQUAST + bunya: '' + description: Quality assessment tool for de novo transcriptome assemblies. + edam-inputs: [] + edam-operations: + - De-novo assembly + - Transcriptome assembly + - Sequence assembly validation + edam-outputs: [] + edam-topics: + - Sequence assembly + - Transcriptomics + - RNA-seq + galaxy: + - description: 'rnaQUAST: A quality assessment tool for De Novo transcriptome assemblies' + title: rnaQUAST 2.2.3+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Frnaquast%2Frna_quast%2F2.2.3%2Bgalaxy0 + homepage: http://cab.spbu.ru/software/rnaquast/ + id: rnaquast + license: Unlicense + name: rnaQUAST + nci-gadi: '' + nci-if89: '' + pawsey: '' + publications: + - title: 'RnaQUAST: A quality assessment tool for de novo transcriptome assemblies' + url: https://doi.org/10.1093/bioinformatics/btw218 + resources: + - title: .nan + url: .nan - biocontainers: roary biotools: roary bunya: '' @@ -20246,6 +20510,12 @@ - Sequencing - Rare diseases galaxy: + - description: 'Samtools markdup: marks duplicate alignments' + title: Samtools markdup 1.15.1+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsamtools_markdup%2Fsamtools_markdup%2F1.15.1%2Bgalaxy2 + - description: 'Samtools coverage: computes the depth at each position or region' + title: Samtools coverage 1.15.1+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsamtools_coverage%2Fsamtools_coverage%2F1.15.1%2Bgalaxy2 - description: 'Samtools split: BAM dataset on readgroups' title: Samtools split 1.15.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fsamtools_split%2Fsamtools_split%2F1.15.1%2Bgalaxy2 @@ -20304,6 +20574,10 @@ - description: 'Samtools depth: compute the depth at each position or region' title: Samtools depth 1.15.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsamtools_depth%2Fsamtools_depth%2F1.15.1%2Bgalaxy2 + - description: 'Samtools fixmate: fill mate coordinates, ISIZE and mate related + flags' + title: Samtools fixmate 1.15.1+galaxy2 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsamtools_fixmate%2Fsamtools_fixmate%2F1.15.1%2Bgalaxy2 - description: 'samtools BAM to CRAM: convert BAM alignments to CRAM format' title: samtools BAM to CRAM 1.15.1+galaxy2 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsamtools_bam_to_cram%2Fsamtools_bam_to_cram%2F1.15.1%2Bgalaxy2 @@ -20947,6 +21221,54 @@ - description: 'Seurat: - toolkit for exploration of single-cell RNA-seq data' title: Seurat 4.3.0.1+galaxy1 url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fseurat%2Fseurat%2F4.3.0.1%2Bgalaxy1 + - description: 'Seurat ScaleData: scale and center genes' + title: Seurat ScaleData 4.0.4+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_scale_data%2Fseurat_scale_data%2F4.0.4%2Bgalaxy0 + - description: 'Seurat RunTSNE: run t-SNE dimensionality reduction' + title: Seurat RunTSNE 4.0.4+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_run_tsne%2Fseurat_run_tsne%2F4.0.4%2Bgalaxy0 + - description: 'Seurat RunPCA: run a PCA dimensionality reduction' + title: Seurat RunPCA 4.0.4+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_run_pca%2Fseurat_run_pca%2F4.0.4%2Bgalaxy0 + - description: 'Seurat Read10x: Loads Tabular or 10x data into a serialized seurat + R object' + title: Seurat Read10x 4.0.4+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_read10x%2Fseurat_read10x%2F4.0.4%2Bgalaxy0 + - description: 'Plot: with Seurat' + title: Plot 4.0.4+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_plot%2Fseurat_plot%2F4.0.4%2Bgalaxy0 + - description: 'Seurat FindVariableGenes: identify variable genes' + title: Seurat FindVariableGenes 4.0.4+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_find_variable_genes%2Fseurat_find_variable_genes%2F4.0.4%2Bgalaxy0 + - description: 'Seurat FindNeighbours: constructs a Shared Nearest Neighbor (SNN) + Graph' + title: Seurat FindNeighbours 4.0.4+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_find_neighbours%2Fseurat_find_neighbours%2F4.0.4%2Bgalaxy0 + - description: 'Seurat FindMarkers: find markers (differentially expressed genes)' + title: Seurat FindMarkers 4.0.4+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_find_markers%2Fseurat_find_markers%2F4.0.4%2Bgalaxy0 + - description: 'Seurat FilterCells: filter cells in a Seurat object' + title: Seurat FilterCells 4.0.4+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_filter_cells%2Fseurat_filter_cells%2F4.0.4%2Bgalaxy0 + - description: 'Seurat Export2CellBrowser: produces files for UCSC CellBrowser import.' + title: Seurat Export2CellBrowser 4.0.4+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_export_cellbrowser%2Fseurat_export_cellbrowser%2F4.0.4%2Bgalaxy0 + - description: 'Seurat CreateSeuratObject: create a Seurat object' + title: Seurat CreateSeuratObject 2.3.1+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_create_seurat_object%2Fseurat_create_seurat_object%2F2.3.1%2Bgalaxy0 + - description: 'Seurat Plot dimension reduction: graphs the output of a dimensional + reduction technique (PCA by default). Cells are colored by their identity class.' + title: Seurat Plot dimension reduction 4.0.4+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_dim_plot%2Fseurat_dim_plot%2F4.0.4%2Bgalaxy0 + - description: 'Seurat FindClusters: find clusters of cells' + title: Seurat FindClusters 4.0.4+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_find_clusters%2Fseurat_find_clusters%2F4.0.4%2Bgalaxy0 + - description: 'Seurat NormaliseData: normalise data' + title: Seurat NormaliseData 4.0.4+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_normalise_data%2Fseurat_normalise_data%2F4.0.4%2Bgalaxy0 + - description: 'Seurat UMAP: dimensionality reduction' + title: Seurat UMAP 4.0.4+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Febi-gxa%2Fseurat_run_umap%2Fseurat_run_umap%2F4.0.4%2Bgalaxy0 homepage: https://satijalab.org/seurat/ id: seurat license: MIT @@ -24553,6 +24875,14 @@ - Data visualisation - Metabolomics galaxy: + - description: 'xcms plot raw: Plot raw data filtered by m/z range and retention + time (RT) range' + title: xcms plot raw 4.0.0+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fworkflow4metabolomics%2Fxcms_plot_raw%2Fxcms_plot_raw%2F4.0.0%2Bgalaxy0 + - description: 'xcms plot eic: Plot the extracted ion chromatogram (EIC) from mzML + file' + title: xcms plot eic 4.0.0+galaxy0 + url: https://usegalaxy.org.au/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fworkflow4metabolomics%2Fxcms_plot_eic%2Fxcms_plot_eic%2F4.0.0%2Bgalaxy0 - description: 'xcms get a sampleMetadata file: which need to be filled with extra information' title: xcms get a sampleMetadata file 3.4.4.0