201809 usegalaxy.org updated tool/version

tools.rst

Tool ID	Version
bam_to_sam	2.0.1
bam_to_scidx	1.0.1
bamSplit	2.4.0
bedtools_coveragebed	2.27
bedtools_intersectbed	2.27
bg_diamond	0.8.24.1
bg_diamond_makedb	0.8.24
blastxml_to_tabular	0.3.0
collection_column_join	0.0.3
count_gff_features	0.2
cshl_fastq_quality_filter	1.0.2
cshl_fastx_clipper	1.0.3
cshl_fastx_reverse_complement	1.0.2
cshl_fastx_trimmer	1.0.2
deeptools_bam_compare	3.1.2
deeptools_bam_coverage	3.1.2
deeptools_bam_pe_fragmentsize	3.1.2
deeptools_bigwig_compare	3.1.2
deeptools_compute_gc_bias	3.1.2
deeptools_compute_matrix	3.1.2
deeptools_correct_gc_bias	3.1.2
deeptools_multi_bam_summary	3.1.2
deeptools_multi_bigwig_summary	3.1.2
deeptools_plot_correlation	3.1.2
deeptools_plot_coverage	3.1.2
deeptools_plot_enrichment	3.1.2
deeptools_plot_fingerprint	3.1.2
deeptools_plot_heatmap	3.1.2
deeptools_plot_pca	3.1.2
deeptools_plot_profile	3.1.2
dexseq	1.24
fasta_nucleotide_changer	1.0.2
fastq_to_fasta	1.0.2
featurecounts	1.6.2
flash	1.2.11.3
gemini_actionable_mutations	0.18.1.0
gemini_amend	0.18.1.0
gemini_annotate	0.18.1.1
gemini_comp_hets	0.18.1.0
gemini_db_info	0.18.1.0
gemini_de_novo	0.18.1.0
gemini_dump	0.18.1.0
gemini_fusions	0.18.1.0
gemini_gene_wise	0.18.1.0
gemini_interactions	0.18.1.0
gemini_load	0.18.1.0
gemini_lof_sieve	0.18.1.0
gemini_mendel_errors	0.18.1.0
gemini_pathways	0.18.1.0
gemini_qc	0.18.1.0
gemini_query	0.18.1.0
gemini_recessive_and_dominant	0.18.1.0
gemini_region	0.18.1.0
gemini_roh	0.18.1.0
gemini_set_somatic	0.18.1.0
gemini_stats	0.18.1.0
gemini_windower	0.18.1.0
genetrack	1.0.1
ggplot2_heatmap2	2.2.1.galaxy1
hisat2	2.1.0+galaxy3
iuc_pear	0.9.6.1
kraken	1.2.4
kraken-mpa-report	1.2.4
kraken-report	1.2.4
limma_voom	3.34.9.8
macs2_bdgdiff	2.1.1.20160309.1
macs2_callpeak	2.1.1.20160309.4
meme_fimo	4.12.0.0
meme_meme	4.12.0.0
multiqc	1.6
ncbi_blastdbcmd_info	0.3.0
ncbi_blastdbcmd_wrapper	0.3.0
ncbi_blastn_wrapper	0.3.0
ncbi_blastp_wrapper	0.3.0
ncbi_blastx_wrapper	0.3.0
ncbi_convert2blastmask_wrapper	0.3.0
ncbi_dustmasker_wrapper	0.3.0
ncbi_makeblastdb	0.3.0
ncbi_makeprofiledb	0.3.0
ncbi_rpsblast_wrapper	0.3.0
ncbi_rpstblastn_wrapper	0.3.0
ncbi_segmasker_wrapper	0.3.0
ncbi_tblastn_wrapper	0.3.0
ncbi_tblastx_wrapper	0.3.0
ngsutils_bam_filter	0.5.9
picard_AddCommentsToBam	2.18.2
picard_AddOrReplaceReadGroups	2.18.2
picard_BedToIntervalList	2.18.2
picard_CASM	2.18.2
picard_CleanSam	2.18.2
picard_CollectBaseDistributionByCycle	2.18.2
picard_CollectGcBiasMetrics	2.18.2
picard_CollectInsertSizeMetrics	2.18.2
picard_CollectRnaSeqMetrics	2.18.2
picard_CollectWgsMetrics	2.18.2
picard_DownsampleSam	2.18.2
picard_EstimateLibraryComplexity	2.18.2
picard_FastqToSam	2.18.2
picard_FilterSamReads	2.18.2
picard_FixMateInformation	2.18.2
picard_MarkDuplicates	2.18.2
picard_MarkDuplicatesWithMateCigar	2.18.2
picard_MeanQualityByCycle	2.18.2
picard_MergeBamAlignment	2.18.2
picard_MergeSamFiles	2.18.2
picard_NormalizeFasta	2.18.2
picard_QualityScoreDistribution	2.18.2
picard_ReorderSam	2.18.2
picard_ReplaceSamHeader	2.18.2
picard_RevertOriginalBaseQualitiesAndAddMateCigar	2.18.2
picard_RevertSam	2.18.2
picard_SamToFastq	2.18.2
picard_SortSam	2.18.2
picard_ValidateSamFile	2.18.2
prokka	1.13
rgweblogo3	3.5.0
salmon	0.11.2
samtool_filter2	1.8
samtools_flagstat	2.0.1
samtools_mpileup	2.1.4
samtools_sort	2.0.2
snpEff_download	4.3+T.galaxy2
snpEff_get_chr_names	4.3+T.galaxy1
stringtie	1.3.4
stringtie_merge	1.3.4
taxonomy_krona_chart	2.6.1.1
tp_awk_tool	1.1.1
tp_grep_tool	1.1.1
tp_replace_in_column	1.1.2
tp_replace_in_line	1.1.1
tp_sed_tool	1.1.1
tp_sort_header_tool	1.1.1
tp_unfold_column_tool	1.1.1
tp_uniq_tool	1.1.1
unicycler	0.4.6.0
varscan	2.4.2
vcfdistance	1.0.0_rc1.0
vegan_diversity	2.4-3
vegan_fisher_alpha	2.4-3
vegan_rarefaction	2.4-3
vsearch_alignment	2.8.3.0
vsearch_chimera_detection	2.8.3.0
vsearch_clustering	2.8.3.0
vsearch_dereplication	2.8.3.0
vsearch_masking	2.8.3.0
vsearch_search	2.8.3.0
vsearch_shuffling	2.8.3.0
vsearch_sorting	2.8.3.0