May 2017 Tool Shed contributions

Tools contributed to the Galaxy Project Tool Shed in May 2017.

• All monthly summaries

New Tools

• From nml:

  • neptune: Neptune Signature Discovery.

• From moba:

  • alvis_rep: tools from the Alvis Framework.

• From sjung:

  • bdds: BDDS Platform and Tool Suite for DNA footprinting. Fseq/Wellington, hint and piq are used for DNA footprinting.

• From earlhaminst:

  • replace_chromosome_names: Replace chromosome names in a tabular dataset using a mapping table.
  • rdock: small molecule - protein docking. A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids.

• From yguitton:

  • withinvariation: v0.4. [Metabolomics][W4M][Statistics] mixOmics R package withinVariation function for repeated mesurement design. This function decomposes the within from the between variance in the data sets X (and Y ) via the internal functions withinVarition(). Once the within variance is calculated, we can run the classical multivariate approaches, such as PCA, PLS-DA and PLS on the within- subject deviation.

• From galaxyp:

  • hirieftools: HiRIEF tools. High resolution isoelectric focusing is a prefractionation technique for shotgun proteomics/mass spectrometry in which peptides are focused along a pI gradient. These tools enable pI-based annotation and database preparation for HiRIEF experiments.
  • psm_to_sam: PSM to SAM. The interpretation of proteomics data is significantly enhanced by genomic annotation. Using proBAMr, peptide-spectrum-matches can be easily reannotated using user-specified gene annotation schemes and assembled into both protein and gene identifications. Using the genome as a common reference, proBAMr facilitates seamless proteomics and proteogenomics data integration. ProBAM files can be readily visualized in genome browsers and thus bring proteomics data analysis to a general audience beyond the proteomics community.
  • apostl: APOSTL Workflows. Workflows for APOSTL Paper.

• From bgruening:

  • shape_it: Shape-it is a tool that aligns a reference molecule against a set of database molecules using the shape of the molecules as the align criterion. It is based on the use of gaussian volumes as descriptor for molecular shape_ as it was introduced by Grant and Pickup. Home page License: GPL3+.
  • openbabel_remduplicates: Remove duplicated molecules tool from Open Babel chemical toolbox. Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Home page License: GPL Version 2.
  • openbabel_subsearch: Substructure Search tool from Open Babel chemical toolbox.
  • strip_it: Strip-it is a program that extracts predefined scaffolds from organic small molecules. Strip-it is a program that extracts predefined scaffolds from organic small molecules.
  • openbabel_remsmall: Remove small molecules tool from Open Babel chemical toolbox.
  • openbabel_compound_convert: Compound Convert tool from Open Babel chemical toolbox.
  • openbabel_spectrophore_search: Spectrophores(TM) search: tool from Open Babel chemical toolbox.
  • ctb_rdkit_describtors: Descriptors tool from RDKit. RDKit is a collection of cheminformatics and machine-learning software. Home page: https://github.com/rdkit/rdkit License: BSD.
  • openbabel_genprop: Compute physico-chemical properties tool from Open Babel chemical toolbox.
  • qed: Estimates the drug-likeness of molecules and reports a score. Estimates the drug-likeness of molecules and reports a score. License: GPL3+.
  • openbabel_obgrep: Compound Search tool from Open Babel chemical toolbox.
  • openbabel_addh: Add hydrogen atoms tool from Open Babel chemical toolbox.
  • openbabel_remions: Remove counterions and fragments tool from Open Babel chemical toolbox.
  • openbabel_svg_depiction: Visualisation tool from Open Babel chemical toolbox.
  • openbabel_filter: Filter tool from Open Babel chemical toolbox.
  • openbabel_change_title: Change Title tool from Open Babel chemical toolbox.
  • openbabel_multi_obgrep: Multi Compound Search tool from Open Babel chemical toolbox.
  • align_it: Align-it is a tool to align molecules according to their pharmacophores. Align-it is a tool to align molecules according to their pharmacophores. A pharmacophore is an abstract concept based on the specific interactions observed in drug-receptor interactions: hydrogen bonding, charge transfer, electrostatic and hydrophobic interactions. Molecular modeling and/or screening based on pharmacophore similarities has been proven to be an important and useful method in drug discovery. Home page: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/align-it/1.0.4/align-it.html License: GPL3+.
  • openbabel_remove_protonation_state: Remove protonation state tool from Open Babel chemical toolbox.

• From marie-tremblay-metatoul:

  • nmr_preprocessing: [W4M][NMR] NMR Preprocessing - Preprocessing (from FID to baseline correction). Part of the W4M project: http://workflow4metabolomics.org.

• From yating-l:

  • multi_fasta_glimmer_hmm: GlimmerHMM is a gene finder based on a Generalized Hidden Markov Model (GHMM).
  • blastxmltopsl: convert blast XML output to PSLs.
  • windowmasker_2_5_0: Identify repetitive regions using WindowMasker. WindowMasker identifies repetitive sequences and low complexity regions within a genome assembly. WindowMasker works in two stages. In stage 1, mkcount produces a unit counts file for a genome assembly. In stage 2, ustat uses the unit counts file to mask repeats in the genome assembly. See Morgulis A, 2006 (PMID: 16287941) for details.
  • trfbig: Mask tandem repeats on a big sequence file.

• From rnateam:

  • footprint: Find transcription factor footprints. This is a pipeline to find transcription factor footprints in ATAC-seq or DNase-seq data.
  • structure_to_gspan: Convert RNA structure to GSPAN graphs. For each pair of sequence and structure provided in the input file and convert them into GSPAN format graphs.
  • data_manager_sortmerna_database_downloader: SortMeRNA: a sequence analysis tool for filtering, mapping and clustering NGS reads. SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.

• From fabio:

  • iristcga: 20170531. IRIS-TCGA: automatically filter, extract, and integrate different genomic experiments from The Cancer Genome Atlas. IRIS-TCGA is a web service to automatically query, filter, extract and integrate different genomic experiments from The Cancer Genome Atlas. The service is available at http://bioinf.iasi.cnr.it/iristcga/.
  • gdcwebapp: 20170524. GDCWebApp: automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format. GDCWebApp is a web service to automatically query, filter, extract and convert genomic data and clinical information from the Genomic Data Commons portal (GDC) to BED format. It is able to operate on all data types for each programs (TCGA and TARGET) available on GDC. The service is available at http://bioinf.iasi.cnr.it/gdcwebapp/.
  • iwtomics: IWTomics v1.0 uploaded. Interval-Wise Testing for Omics Data. Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.

• From eschen42:

  • w4mclassfilter: Filter W4M data files by class. Filter Workflow4Metabolomics data matrix and metadata by sample-class.

• From drosofff:

  • repenrich: Repeat element profiling. RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.

• From iuc:

  • mothur_get_rabund: Wrapper for mothur application: Get.rabund. The mothur project seeks to offers a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. We have incorporated the functionality of dotur, sons, treeclimber, s-libshuff, unifrac, and much more. In addition to improving the flexibility of these algorithms, we have added a number of other features including calculators and visualization tools.
  • mothur_metastats: Wrapper for mothur application: Metastats.
  • masigpro: Identify significantly differential expression profiles in time-course microarray experiments. maSigPro is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.
  • qiime_pick_rep_set: Wrapper for the qiime tool suite: Pick representative set of sequences. "QIIME: Quantitative Insights Into Microbial Ecology QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data".
  • mothur_sens_spec: Wrapper for mothur application: Sens.spec.
  • mothur_summary_tax: Wrapper for mothur application: Summary.tax.
  • mothur_summary_shared: Wrapper for mothur application: Summary.shared.
  • qiime_filter_alignment: Wrapper for the qiime tool suite: Filter sequence alignment.
  • mothur_heatmap_sim: Wrapper for mothur application: Heatmap.sim.
  • stacks_clonefilter: Stacks: clone filter (from the Stacks tool suite). Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. http://catchenlab.life.illinois.edu/stacks/.
  • data_manager_qiime_database_downloader: QIIME to perform microbial community analysis. QIIME: Quantitative Insights Into Microbial Ecology QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data http://www.qiime.org.
  • mothur_align_check: Wrapper for mothur application: Align.check.
  • mothur_heatmap_bin: Wrapper for mothur application: Heatmap.bin.
  • qiime_make_emperor: Wrapper for the qiime tool suite: Create three-dimensional PCoA plots.
  • qiime_split_libraries: Wrapper for the qiime tool suite: Split libraries.
  • qiime_align_seqs: Wrapper for the qiime tool suite: Align sequences.
  • mothur_chop_seqs: Wrapper for mothur application: Chop.seqs.
  • mothur_chimera_perseus: Wrapper for mothur application: Chimera.perseus.
  • mothur_clearcut: Wrapper for mothur application: Clearcut.
  • mothur_sffinfo: Wrapper for mothur application: Sffinfo.
  • mothur_get_coremicrobiome: Wrapper for mothur application: Get.coremicrobiome.
  • mothur_anosim: Wrapper for mothur application: Anosim.
  • mothur_make_lookup: Wrapper for mothur application: Make.lookup.
  • mothur_get_lineage: Wrapper for mothur application: Get.lineage.
  • samtools_bam_to_cram: Converts alignments in BAM format to CRAM format. This tool uses the SAMtools toolkit to convert BAM to CRAM files. The CRAM format does additional compression relative to the reference genome which makes the compression more efficient in terms of file size.
  • mothur_remove_rare: Wrapper for mothur application: Remove.rare.
  • mothur_parsimony: Wrapper for mothur application: Parsimony.
  • qiime_beta_diversity: Wrapper for the qiime tool suite: Calculate beta diversity.
  • mothur_make_biom: Wrapper for mothur application: Make.biom.
  • mothur_lefse: Wrapper for mothur application: Lefse.
  • mothur_get_relabund: Wrapper for mothur application: Get.relabund.
  • mothur_chimera_uchime: Wrapper for mothur application: Chimera.uchime.
  • mothur_chimera_check: Wrapper for mothur application: Chimera.check.
  • mothur_make_shared: Wrapper for mothur application: Make.shared.
  • mothur_get_seqs: Wrapper for mothur application: Get.seqs.
  • mothur_get_oturep: Wrapper for mothur application: Get.oturep.
  • mothur_shhh_flows: Wrapper for mothur application: Shhh.flows.
  • mothur_unifrac_weighted: Wrapper for mothur application: unifrac.weighted.
  • qiime_compare_categories: Wrapper for the qiime tool suite: Analyzes statistical significance.
  • qiime_assign_taxonomy: Wrapper for the qiime tool suite: Assign taxonomy.
  • mothur_deunique_seqs: Wrapper for mothur application: Deunique.seqs.
  • mothur_classify_otu: Wrapper for mothur application: Classify.otu.
  • mothur_pcoa: Wrapper for mothur application: Pcoa.
  • qiime_pick_closed_reference_otus: Wrapper for the qiime tool suite: Perform closed-reference OTU picking.
  • mothur_merge_taxsummary: Wrapper for mothur application: Merge.taxsummary.
  • mothur_remove_dists: Wrapper for mothur application: Remove.dists.
  • mothur_unifrac_unweighted: Wrapper for mothur application: unifrac.unweighted.
  • qiime_validate_mapping_file: Wrapper for the qiime tool suite: Validate mapping file.
  • mothur_pairwise_seqs: Wrapper for mothur application: Pairwise.seqs.
  • mothur_bin_seqs: Wrapper for mothur application: Bin.seqs.
  • mothur_make_design: Wrapper for mothur application: Make Design.
  • mothur_get_sabund: Wrapper for mothur application: Get.sabund.
  • qiime_filter_fasta: Wrapper for the qiime tool suite: Filter fasta.
  • mothur_cluster_split: Wrapper for mothur application: Cluster.split.
  • mothur_remove_otus: Wrapper for mothur application: Remove.otus.
  • mothur_make_group: Wrapper for mothur application: Make.group.
  • mothur_venn: Wrapper for mothur application: Venn.
  • mothur_collect_shared: Wrapper for mothur application: Collect.shared.
  • mothur_chimera_ccode: Wrapper for mothur application: Chimera.ccode.
  • qiime_plot_taxa_summary: Wrapper for the qiime tool suite: Make taxonomy summary charts.
  • mothur_phylotype: Wrapper for mothur application: Phylotype.
  • mothur_split_abund: Wrapper for mothur application: Split.abund.
  • mothur_fastq_info: Wrapper for mothur application: Fastq.info.
  • mothur_hcluster: Wrapper for mothur application: Hcluster.
  • mothur_list_otulabels: Wrapper for mothur application: List.otulabels.
  • mothur_chimera_slayer: Wrapper for mothur application: Chimera.slayer.
  • mothur_get_dists: Wrapper for mothur application: Get.dists.
  • mothur_merge_files: Wrapper for mothur application: Merge.files.
  • mothur_dist_shared: Wrapper for mothur application: Dist.shared.
  • mothur_trim_flows: Wrapper for mothur application: Trim.flows.
  • mothur_get_otulist: Wrapper for mothur application: Get.otulist.
  • qiime_count_seqs: Wrapper for the qiime tool suite: Count sequences.
  • mothur_cooccurrence: Wrapper for mothur application: Cooccurrence.
  • mothur_get_group: Wrapper for mothur application: Get.group.
  • mothur_summary_seqs: Wrapper for mothur application: Summary.seqs.
  • mothur_get_sharedseqs: Wrapper for mothur application: Get.sharedseqs.
  • mothur_make_sra: Wrapper for mothur application: Make.sra.
  • mothur_filter_seqs: Wrapper for mothur application: Filter.seqs.
  • mothur_get_label: Wrapper for mothur application: Get.label.
  • mothur_sort_seqs: Wrapper for mothur application: Sort.seqs.
  • qiime_summarize_taxa: Wrapper for the qiime tool suite: Summarize taxa.
  • mothur_unique_seqs: Wrapper for mothur application: Unique.seqs.
  • mothur_primer_design: Wrapper for mothur application: Primer.design.
  • mothur_remove_lineage: Wrapper for mothur application: Remove.lineage.
  • mothur_classify_rf: Wrapper for mothur application: Classify.rf.
  • mothur_rarefaction_shared: Wrapper for mothur application: Rarefaction.shared.
  • mothur_get_otulabels: Wrapper for mothur application: Get.otulabels.
  • mothur_tree_shared: Wrapper for mothur application: Tree.shared.
  • mothur_get_groups: Wrapper for mothur application: Get.groups.
  • mothur_mantel: Wrapper for mothur application: Mantel.
  • mothur_screen_seqs: Wrapper for mothur application: Screen.seqs.
  • mothur_pca: Wrapper for mothur application: Pca.
  • mothur_consensus_seqs: Wrapper for mothur application: Consensus.seqs.
  • mothur_merge_sfffiles: Wrapper for mothur application: Merge.sfffiles.
  • mothur_amova: Wrapper for mothur application: Amova.
  • qiime_upgma_cluster: Wrapper for the qiime tool suite: Build UPGMA tree.
  • mothur_list_seqs: Wrapper for mothur application: List.seqs.
  • mothur_rarefaction_single: Wrapper for mothur application: Rarefaction.single.
  • mothur_count_groups: Wrapper for mothur application: Count.groups.
  • mothur_seq_error: Wrapper for mothur application: Seq.error.
  • mothur_split_groups: Wrapper for mothur application: Split.groups.
  • mothur_remove_otulabels: Wrapper for mothur application: Remove.otulabels.
  • mothur_chimera_bellerophon: Wrapper for mothur application: Chimera.bellerophon.
  • mothur_nmds: Wrapper for mothur application: Nmds.
  • mothur_corr_axes: Wrapper for mothur application: Corr.axes.
  • mothur_parse_list: Wrapper for mothur application: Parse.list.
  • mothur_indicator: Wrapper for mothur application: Indicator.
  • mothur_get_otus: Wrapper for mothur application: Get.otus.
  • mothur_dist_seqs: Wrapper for mothur application: Dist.seqs.
  • mothur_align_seqs: Wrapper for mothur application: Align.seqs.
  • mothur_create_database: Wrapper for mothur application: Create.database.
  • qiime_core_diversity: Wrapper for the qiime tool suite: Compute core set of diversity analyses.
  • mothur_phylo_diversity: Wrapper for mothur application: Phylo.diversity.
  • qiime_filter_otus_from_otu_table: Wrapper for the qiime tool suite: Filter otus from otu table.
  • mothur_pre_cluster: Wrapper for mothur application: Pre.cluster.
  • mothur_make_lefse: Wrapper for mothur application: Make.lefse.
  • mothur_summary_single: Wrapper for mothur application: Summary.single.
  • qiime_beta_diversity_through_plots: Wrapper for the qiime tool suite: Compute beta diversity distance matrices.
  • mothur_cluster_classic: Wrapper for mothur application: Cluster.classic.
  • qiime_jackknifed_beta_diversity: Wrapper for the qiime tool suite: Perform jackknifed UPGMA clustering.
  • qiime_multiple_join_paired_ends: Wrapper for the qiime tool suite: Join paired-end Illumina reads.
  • mothur_cluster_fragments: Wrapper for mothur application: Cluster.fragments.
  • mothur_classify_tree: Wrapper for mothur application: Classify.tree.
  • mothur_degap_seqs: Wrapper for mothur application: Degap.seqs.
  • qiime_make_phylogeny: Wrapper for the qiime tool suite: Make phylogeny.
  • qiime_split_libraries_fastq: Wrapper for the qiime tool suite: Split fastq libraries.
  • mothur_libshuff: Wrapper for mothur application: Libshuff.
  • qiime_alpha_diversity: Wrapper for the qiime tool suite: Calculate alpha diversity.
  • qiime_summarize_taxa_through_plots: Wrapper for the qiime tool suite: Perform taxonomy.
  • mothur_normalize_shared: Wrapper for mothur application: Normalize.shared.
  • mothur_sub_sample: Wrapper for mothur application: Sub.sample.
  • mothur_filter_shared: Wrapper for mothur application: Filter.shared.
  • mothur_trim_seqs: Wrapper for mothur application: Trim.seqs.
  • mothur_merge_groups: Wrapper for mothur application: Merge.groups.
  • qiime_make_otu_heatmap: Wrapper for the qiime tool suite: Plot heatmap of OTU table.
  • mothur_remove_groups: Wrapper for mothur application: Remove.groups.
  • mothur_pcr_seqs: Wrapper for mothur application: Pcr.seqs.
  • mothur_mimarks_attributes: Wrapper for mothur application: Get.mimarkspackage.
  • mothur_count_seqs: Wrapper for mothur application: Count.seqs.
  • mothur_summary_qual: Wrapper for mothur application: Summary.qual.
  • mothur_otu_hierarchy: Wrapper for mothur application: Otu.hierarchy.
  • qiime_alpha_rarefaction: Wrapper for the qiime tool suite: Perform alpha rarefaction.
  • mothur_collect_single: Wrapper for mothur application: Collect.single.
  • mothur_shhh_seqs: Wrapper for mothur application: Shhh.seqs.
  • mothur_otu_association: Wrapper for mothur application: Otu.association.
  • mothur_chimera_pintail: Wrapper for mothur application: Chimera.pintail.
  • mothur_make_fastq: Wrapper for mothur application: Make.fastq.
  • mothur_classify_seqs: Wrapper for mothur application: Classify.seqs.
  • qiime_multiple_split_libraries_fastq: Wrapper for the qiime tool suite: Split multiple FastQ librairies.
  • mothur_make_contigs: Wrapper for mothur application: Make.contigs.
  • mothur_reverse_seqs: Wrapper for mothur application: Reverse.seqs.
  • qiime_filter_samples_from_otu_table: Wrapper for the qiime tool suite: Filters samples from an OTU table.
  • mothur_remove_seqs: Wrapper for mothur application: Remove.seqs.
  • qiime_pick_open_reference_otus: Wrapper for the qiime tool suite: Perform open-reference OTU picking.
  • samtools_cram_to_bam: Converts alignments in CRAM format to BAM format. This tool uses the SAMtools toolkit to convert CRAM to BAM files.
  • mothur_homova: Wrapper for mothur application: Homova.
  • mothur_deunique_tree: Wrapper for mothur application: Deunique.tree.
  • qiime_filter_taxa_from_otu_table: Wrapper for the qiime tool suite: Filter taxa from otu table.
  • mothur_get_communitytype: Wrapper for mothur application: Get.communitytype.
  • qiime_pick_otus: Wrapper for the qiime tool suite: Pick OTUs.
  • mothur_cluster: Wrapper for mothur application: Cluster.
  • mothur_get_mimarkspackage: Wrapper for mothur application: Get.mimarkspackage.

• From jasper:

  • dna_protein_transle: Translate DNA to protein. Translate nucleic acid to protein.