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tools.txt
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# ../training-material/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.md
## ../training-material/topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing_and_sra_download.ga
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0
toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7
toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.4+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2
## ../training-material/topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing.ga
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0
toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7
toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2
# ../training-material/topics/assembly/tutorials/chloroplast-assembly/tutorial.md
## ../training-material/topics/assembly/tutorials/chloroplast-assembly/workflows/Galaxy-Workflow-Chloroplast-genome-assembly-and-annotation.ga
toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.3.7
toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.9+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.28.2+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/pilon/pilon/1.20.1
toolshed.g2.bx.psu.edu/repos/simon-gladman/fasta_stats/fasta-stats/1.0.0
# ../training-material/topics/climate/tutorials/fates/tutorial.md
# ../training-material/topics/computational-chemistry/tutorials/cheminformatics/tutorial.md
## ../training-material/topics/computational-chemistry/tutorials/cheminformatics/workflows/main_workflow.ga
toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_mol2fps/0.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_nxn_clustering/0.4
toolshed.g2.bx.psu.edu/repos/bgruening/chemical_data_sources/ctb_online_data_fetch/0.2
toolshed.g2.bx.psu.edu/repos/bgruening/natural_product_likeness/ctb_np-likeness-calculator/2.1
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_change_title/0.0.1
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_compound_convert/0.1
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_filter/1.0
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_obgrep/0.1
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_remDuplicates/1.0
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_remIons/1.0
# ../training-material/topics/computational-chemistry/tutorials/md-simulation-gromacs/tutorial.md
## ../training-material/topics/computational-chemistry/tutorials/md-simulation-gromacs/workflows/main_workflow.ga
toolshed.g2.bx.psu.edu/repos/bgruening/get_pdb/get_pdb/0.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2020.2+galaxy0
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2020.2+galaxy0
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2020.2+galaxy0
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2020.2+galaxy0
toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2020.2+galaxy0
# ../training-material/topics/ecology/tutorials/PAMPA-toolsuite-tutorial/tutorial.md
# ../training-material/topics/epigenetics/tutorials/atac-seq/tutorial.md
## ../training-material/topics/epigenetics/tutorials/atac-seq/workflows/main_workflow.ga
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/3.0.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.0.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.1
toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectInsertSizeMetrics/2.18.2.1
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2
toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.29.0
toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_sortbed/2.29.2
toolshed.g2.bx.psu.edu/repos/iuc/genrich/genrich/0.5+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.6
toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.3
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5
# ../training-material/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.md
## ../training-material/topics/genome-annotation/tutorials/annotation-with-prokka/workflows/Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga
toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.5+galaxy7
# ../training-material/topics/introduction/tutorials/galaxy-intro-101/tutorial.md
## ../training-material/topics/introduction/tutorials/galaxy-intro-101/workflows/galaxy-intro-101-workflow.ga
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1
toolshed.g2.bx.psu.edu/repos/devteam/join/gops_join_1/0.0.1
# ../training-material/topics/introduction/tutorials/r-advanced/tutorial.md
# ../training-material/topics/introduction/tutorials/r-basics/tutorial.md
# ../training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.md
## ../training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/workflows/workflow1_quality_control.ga
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0
toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.0
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0
toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0
## ../training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/workflows/workflow2_data_cleaning.ga
toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_vsearch/mothur_chimera_vsearch/1.39.5.1
toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_seqs/mothur_filter_seqs/1.39.5.0
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pre_cluster/mothur_pre_cluster/1.39.5.0
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_seqs/mothur_remove_seqs/1.36.1.0
toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.0
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0
toolshed.g2.bx.psu.edu/repos/iuc/mothur_unique_seqs/mothur_unique_seqs/1.39.5.0
## ../training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/workflows/workflow3_classification.ga
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_seqs/mothur_classify_seqs/1.39.5.0
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.39.5.0
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_seqs/mothur_summary_seqs/1.39.5.0
## ../training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/workflows/workflow4_mock_otu_clustering.ga
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster/mothur_cluster/1.39.5.0
toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_seqs/mothur_dist_seqs/1.39.5.0
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0
toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0
## ../training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/workflows/workflow5_otu_clustering.ga
toolshed.g2.bx.psu.edu/repos/iuc/mothur_classify_otu/mothur_classify_otu/1.39.5.0
toolshed.g2.bx.psu.edu/repos/iuc/mothur_cluster_split/mothur_cluster_split/1.39.5.0
toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_groups/mothur_count_groups/1.39.5.0
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.39.5.0
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_groups/mothur_remove_groups/1.39.5.0
toolshed.g2.bx.psu.edu/repos/iuc/mothur_sub_sample/mothur_sub_sample/1.39.5.0
## ../training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/workflows/workflow6_alpha_diversity.ga
toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.2
toolshed.g2.bx.psu.edu/repos/iuc/mothur_rarefaction_single/mothur_rarefaction_single/1.39.5.0
toolshed.g2.bx.psu.edu/repos/iuc/mothur_summary_single/mothur_summary_single/1.39.5.0
## ../training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/workflows/workflow7_beta_diversity.ga
toolshed.g2.bx.psu.edu/repos/iuc/mothur_dist_shared/mothur_dist_shared/1.39.5.0
toolshed.g2.bx.psu.edu/repos/iuc/mothur_heatmap_sim/mothur_heatmap_sim/1.39.5.0
toolshed.g2.bx.psu.edu/repos/iuc/mothur_tree_shared/mothur_tree_shared/1.39.5.0
toolshed.g2.bx.psu.edu/repos/iuc/mothur_venn/mothur_venn/1.39.5.0
toolshed.g2.bx.psu.edu/repos/iuc/newick_utils/newick_display/1.6
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.0
# ../training-material/topics/metagenomics/tutorials/nanopore-16S-metagenomics/tutorial.md
## ../training-material/topics/metagenomics/tutorials/nanopore-16S-metagenomics/workflows/main_workflow.ga
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2
toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse/1.1.0
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.0.8_beta+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3
# ../training-material/topics/proteomics/tutorials/biomarker_selection/tutorial.md
## ../training-material/topics/proteomics/tutorials/biomarker_selection/workflows/main_workflow.ga
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.0.0
toolshed.g2.bx.psu.edu/repos/proteore/proteore_expression_rnaseq_abbased/rna_abbased_data/2019.03.07
toolshed.g2.bx.psu.edu/repos/proteore/proteore_filter_keywords_values/MQoutputfilter/2019.03.05
toolshed.g2.bx.psu.edu/repos/proteore/proteore_id_converter/IDconverter/2019.01.28
toolshed.g2.bx.psu.edu/repos/proteore/proteore_ms_observation_pepatlas/retr_pepatlas1/2019.02.01.1
toolshed.g2.bx.psu.edu/repos/proteore/proteore_prot_features/prot_features/2019.01.18
toolshed.g2.bx.psu.edu/repos/proteore/proteore_tissue_specific_expression_data/retrieve_from_hpa/2019.02.27
toolshed.g2.bx.psu.edu/repos/proteore/proteore_venn_diagram/Jvenn/2018.12.18
# ../training-material/topics/proteomics/tutorials/metaproteomics/tutorial.md
## ../training-material/topics/proteomics/tutorials/metaproteomics/workflows/workflow.ga
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1
toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept/4.3.0
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0
toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0
# ../training-material/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.md
## ../training-material/topics/proteomics/tutorials/proteogenomics-dbcreation/workflows/galaxy-workflow-mouse_rnaseq_dbcreation.ga
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3
toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab/1.1.0
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/1.3.1
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.0
toolshed.g2.bx.psu.edu/repos/galaxyp/bed_to_protein_map/bed_to_protein_map/0.2.0
toolshed.g2.bx.psu.edu/repos/galaxyp/custom_pro_db/custom_pro_db/1.22.0
toolshed.g2.bx.psu.edu/repos/galaxyp/fasta_merge_files_and_filter_unique_sequences/fasta_merge_files_and_filter_unique_sequences/1.2.0
toolshed.g2.bx.psu.edu/repos/galaxyp/gffcompare_to_bed/gffcompare_to_bed/0.2.1
toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.0
toolshed.g2.bx.psu.edu/repos/galaxyp/translate_bed/translate_bed/0.1.0
toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0
toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare/0.11.2
toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0+galaxy5
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0
toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular/2.0.0
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1
# ../training-material/topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.md
## ../training-material/topics/proteomics/tutorials/proteogenomics-dbsearch/workflows/galaxy-workflow-mouse_rnaseq_dbsearch.ga
toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.0
toolshed.g2.bx.psu.edu/repos/galaxyp/mz_to_sqlite/mz_to_sqlite/2.0.4+galaxy1
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3
toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/search_gui/3.3.10.1
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0
# ../training-material/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/tutorial.md
## ../training-material/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/workflows/galaxy-workflow-mouse_novel_peptide_analysis.ga
toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/0.3.3
toolshed.g2.bx.psu.edu/repos/galaxyp/pep_pointer/pep_pointer/0.1.3
toolshed.g2.bx.psu.edu/repos/galaxyp/peptide_genomic_coordinate/peptide_genomic_coordinate/0.1.1
toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.0.0
# ../training-material/topics/proteomics/tutorials/proteome_annotation/tutorial.md
## ../training-material/topics/proteomics/tutorials/proteome_annotation/workflows/Galaxy-Workflow-_Proteome_annotation_.ga
toolshed.g2.bx.psu.edu/repos/proteore/proteore_clusterprofiler/cluter_profiler/2019.02.18
toolshed.g2.bx.psu.edu/repos/proteore/proteore_expression_rnaseq_abbased/rna_abbased_data/2019.03.07
toolshed.g2.bx.psu.edu/repos/proteore/proteore_filter_keywords_values/MQoutputfilter/2019.03.11
toolshed.g2.bx.psu.edu/repos/proteore/proteore_id_converter/IDconverter/2019.03.07
toolshed.g2.bx.psu.edu/repos/proteore/proteore_reactome/reactome_analysis/2019.03.05
toolshed.g2.bx.psu.edu/repos/proteore/proteore_tissue_specific_expression_data/retrieve_from_hpa/2019.02.27
toolshed.g2.bx.psu.edu/repos/proteore/proteore_venn_diagram/Jvenn/2019.02.21
## ../training-material/topics/proteomics/tutorials/proteome_annotation/workflows/main_workflow.ga
toolshed.g2.bx.psu.edu/repos/proteore/proteore_clusterprofiler/cluter_profiler/2019.02.18
toolshed.g2.bx.psu.edu/repos/proteore/proteore_expression_rnaseq_abbased/rna_abbased_data/2019.03.07
toolshed.g2.bx.psu.edu/repos/proteore/proteore_filter_keywords_values/MQoutputfilter/2019.03.11
toolshed.g2.bx.psu.edu/repos/proteore/proteore_id_converter/IDconverter/2019.03.07
toolshed.g2.bx.psu.edu/repos/proteore/proteore_reactome/reactome_analysis/2018.12.12
toolshed.g2.bx.psu.edu/repos/proteore/proteore_tissue_specific_expression_data/retrieve_from_hpa/2019.02.27
toolshed.g2.bx.psu.edu/repos/proteore/proteore_venn_diagram/Jvenn/2019.02.21
# ../training-material/topics/sequence-analysis/tutorials/mapping/tutorial.md
## ../training-material/topics/sequence-analysis/tutorials/mapping/workflows/mapping.ga
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1
toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.2
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6
## ../training-material/topics/sequence-analysis/tutorials/mapping/workflows/mapping-jbrowse.ga
toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.2
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.1
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.1+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6
# ../training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.md
## ../training-material/topics/sequence-analysis/tutorials/quality-control/workflows/quality_control.ga
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.3
# ../training-material/topics/transcriptomics/tutorials/ref-based/tutorial.md
## ../training-material/topics/transcriptomics/tutorials/ref-based/workflows/deg-analysis.ga
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.2.0
toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.0.1
toolshed.g2.bx.psu.edu/repos/iuc/goseq/goseq/1.36.0+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/pathview/pathview/1.24.0+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/0.9.1
## ../training-material/topics/transcriptomics/tutorials/ref-based/workflows/qc-mapping-counting.ga
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71
toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.2
toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6
toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.6.0b-1
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.1
toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/2.6.4.1
# ../training-material/topics/transcriptomics/tutorials/rna-seq-counts-to-viz-in-r/tutorial.md
# ../training-material/topics/transcriptomics/tutorials/scrna-preprocessing-tenx/tutorial.md
## ../training-material/topics/transcriptomics/tutorials/scrna-preprocessing-tenx/workflows/scrna_tenx.ga
toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9
toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.7a
# ../training-material/topics/transcriptomics/tutorials/scrna-scanpy-pbmc3k/tutorial.md
## ../training-material/topics/transcriptomics/tutorials/scrna-scanpy-pbmc3k/workflows/main_workflow.ga
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.1
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/1.1.0
toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.6.22.post1+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.6.22.post1+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.6.22.post1+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.4.4.post1+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.4.4.post1+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.4.4.post1+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.4.4.post1+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.4.4.post1+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.4.4.post1+galaxy1
# ../training-material/topics/transcriptomics/tutorials/scrna-umis/tutorial.md
# ../training-material/topics/variant-analysis/tutorials/sars-cov-2/tutorial.md
## ../training-material/topics/variant-analysis/tutorials/sars-cov-2/workflows/main_workflow.ga
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19
toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.7+galaxy1
# ../training-material/topics/variant-analysis/tutorials/tb-variant-analysis/tutorial.md
## ../training-material/topics/variant-analysis/tutorials/tb-variant-analysis/workflows/tb-variant-analysis.ga
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.8+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/kraken2/kraken2/2.0.8_beta+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/4.5.0
toolshed.g2.bx.psu.edu/repos/iuc/tbprofiler/tb_profiler_profile/2.8.4+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/tb_variant_filter/tb_variant_filter/0.1.3+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/tbvcfreport/tbvcfreport/0.1.7+galaxy0
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.5
# ../training-material/topics/visualisation/tutorials/jbrowse/tutorial.md