Add citations to all the tools.

[jmchilton]

• [ ] add_value > tools/add_value
• [ ] analyze_covariates > tool_collections/gatk/analyze_covariates
• [ ] annotation_profiler > tools/annotation_profiler
• [x] bamleftalign > tools/freebayes
• [x] bam_to_sam > tool_collections/samtools/bam_to_sam
• [ ] basecoverage > tool_collections/gops/basecoverage
• [ ] best_regression_subsets > tools/best_regression_subsets
• [ ] blat_coverage_report > tools/blat_coverage_report
• [ ] blat_mapping > tools/blat_mapping
• [x] bowtie2 > tools/bowtie2
• [x] bowtie_color_wrappers > tools/bowtie_color_wrappers
• [x] bowtie_wrappers > tools/bowtie_wrappers
• [x] bwa_wrappers > tools/bwa_wrappers
• [ ] canonical_correlation_analysis > tools/canonical_correlation_analysis
• [ ] categorize_elements_satisfying_criteria > tools/categorize_elements_satisfying_criteria
• [ ] ccat > tools/ccat
• [ ] change_case > tools/change_case
• [x] clustalw > tools/clustalw
• [ ] cluster > tool_collections/gops/cluster
• [ ] column_maker > tools/column_maker
• [ ] complement > tool_collections/gops/complement
• [ ] compute_motif_frequencies_for_all_motifs > tools/compute_motif_frequencies_for_all_motifs
• [ ] compute_motifs_frequency > tools/compute_motifs_frequency
• [ ] compute_q_values > tools/compute_q_values
• [ ] concat > tool_collections/gops/concat
• [ ] condense_characters > tools/condense_characters
• [ ] convert_characters > tools/convert_characters
• [ ] convert_solid_color2nuc > tools/convert_solid_color2nuc
• [ ] correlation > tools/correlation
• [ ] count_covariates > tool_collections/gatk/count_covariates
• [ ] count_gff_features > tools/count_gff_features
• [ ] coverage > tool_collections/gops/coverage
• [ ] ctd_batch > tools/ctd_batch
• [x] cuffcompare > tool_collections/cufflinks/cuffcompare
• [x] cuffdiff > tool_collections/cufflinks/cuffdiff
• [x] cufflinks > tool_collections/cufflinks/cufflinks
• [x] cuffmerge > tool_collections/cufflinks/cuffmerge
• [ ] cut_columns > tools/cut_columns
• [ ] delete_overlapping_indels > tools/delete_overlapping_indels
• [ ] depth_of_coverage > tool_collections/gatk/depth_of_coverage
• [ ] dgidb_annotator > tools/dgidb_annotator
• [ ] divide_pg_snp > tools/divide_pg_snp
• [ ] dna_filtering > tools/dna_filtering
• [ ] draw_stacked_barplots > tools/draw_stacked_barplots
• [ ] dwt_cor_ava_perclass > tools/dwt_cor_ava_perclass
• [ ] dwt_cor_avb_all > tools/dwt_cor_avb_all
• [ ] dwt_ivc_all > tools/dwt_ivc_all
• [ ] dwt_var_perclass > tools/dwt_var_perclass
• [ ] dwt_var_perfeature > tools/dwt_var_perfeature
• [ ] emboss_5 > tools/emboss_5
• [ ] express > tools/express
• [ ] fasta_clipping_histogram > tool_collections/fastx_toolkit/fasta_clipping_histogram
• [ ] fasta_compute_length > tools/fasta_compute_length
• [ ] fasta_concatenate_by_species > tools/fasta_concatenate_by_species
• [ ] fasta_filter_by_length > tools/fasta_filter_by_length
• [ ] fasta_formatter > tool_collections/fastx_toolkit/fasta_formatter
• [ ] fasta_nucleotide_changer > tool_collections/fastx_toolkit/fasta_nucleotide_changer
• [ ] fasta_to_tabular > tools/fasta_to_tabular
• [x] fastqc > tools/fastqc
• [ ] fastq_combiner > tool_collections/galaxy_sequence_utils/fastq_combiner
• [ ] fastq_filter > tool_collections/galaxy_sequence_utils/fastq_filter
• [ ] fastq_groomer > tool_collections/galaxy_sequence_utils/fastq_groomer
• [ ] fastq_manipulation > tool_collections/galaxy_sequence_utils/fastq_manipulation
• [ ] fastq_masker_by_quality > tool_collections/galaxy_sequence_utils/fastq_masker_by_quality
• [ ] fastq_paired_end_deinterlacer > tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer
• [ ] fastq_paired_end_interlacer > tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer
• [ ] fastq_paired_end_joiner > tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner
• [ ] fastq_paired_end_splitter > tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter
• [ ] fastq_quality_boxplot > tool_collections/fastx_toolkit/fastq_quality_boxplot
• [ ] fastq_quality_converter > tool_collections/fastx_toolkit/fastq_quality_converter
• [ ] fastq_quality_filter > tool_collections/fastx_toolkit/fastq_quality_filter
• [ ] fastqsolexa_to_fasta_qual > tools/fastqsolexa_to_fasta_qual
• [ ] fastq_stats > tool_collections/galaxy_sequence_utils/fastq_stats
• [ ] fastqtofasta > tool_collections/galaxy_sequence_utils/fastqtofasta
• [ ] fastq_to_fasta > tool_collections/fastx_toolkit/fastq_to_fasta
• [ ] fastq_to_tabular > tool_collections/galaxy_sequence_utils/fastq_to_tabular
• [ ] fastq_trimmer > tool_collections/galaxy_sequence_utils/fastq_trimmer
• [ ] fastq_trimmer_by_quality > tools/fastq_trimmer_by_quality
• [ ] fastx_artifacts_filter > tool_collections/fastx_toolkit/fastx_artifacts_filter
• [ ] fastx_barcode_splitter > tool_collections/fastx_toolkit/fastx_barcode_splitter
• [ ] fastx_clipper > tool_collections/fastx_toolkit/fastx_clipper
• [ ] fastx_collapser > tool_collections/fastx_toolkit/fastx_collapser
• [ ] fastx_nucleotides_distribution > tool_collections/fastx_toolkit/fastx_nucleotides_distribution
• [ ] fastx_quality_statistics > tool_collections/fastx_toolkit/fastx_quality_statistics
• [ ] fastx_renamer > tool_collections/fastx_toolkit/fastx_renamer
• [ ] fastx_reverse_complement > tool_collections/fastx_toolkit/fastx_reverse_complement
• [ ] fastx_trimmer > tool_collections/fastx_toolkit/fastx_trimmer
• [ ] featurecounter > tools/featurecounter
• [ ] filter_transcripts_via_tracking > tools/filter_transcripts_via_tracking
• [ ] find_diag_hits > tool_collections/taxonomy/find_diag_hits
• [ ] flanking_features > tool_collections/gops/flanking_features
• [ ] generate_pc_lda_matrix > tools/generate_pc_lda_matrix
• [ ] get_flanks > tool_collections/gops/get_flanks
• [ ] getindelrates_3way > tools/getindelrates_3way
• [ ] getindels_2way > tools/getindels_2way
• [ ] gi2taxonomy > tool_collections/taxonomy/gi2taxonomy
• [ ] gmaj > tools/gmaj
• [ ] hgv_fundo > tool_collections/hgv/hgv_fundo
• [ ] hgv_hilbertvis > tool_collections/hgv/hgv_hilbertvis
• [ ] histogram > tools/histogram
• [ ] indel_realigner > tool_collections/gatk/indel_realigner
• [ ] indels_3way > tools/indels_3way
• [ ] intersect > tool_collections/gops/intersect
• [ ] join > tool_collections/gops/join
• [ ] kernel_canonical_correlation_analysis > tools/kernel_canonical_correlation_analysis
• [ ] kernel_principal_component_analysis > tools/kernel_principal_component_analysis
• [ ] lastz > tools/lastz
• [ ] lastz_paired_reads > tools/lastz_paired_reads
• [ ] lca_wrapper > tool_collections/taxonomy/lca_wrapper
• [ ] lda_analysis > tools/lda_analysis
• [ ] linear_regression > tools/linear_regression
• [ ] logistic_regression_vif > tools/logistic_regression_vif
• [x] macs > tools/macs
• [ ] maf_cpg_filter > tools/maf_cpg_filter
• [ ] mapping_to_ucsc > tools/mapping_to_ucsc
• [ ] megablast_wrapper > tools/megablast_wrapper
• [ ] megablast_xml_parser > tools/megablast_xml_parser
• [ ] merge > tool_collections/gops/merge
• [ ] merge_cols > tools/merge_cols
• [ ] microsatellite_birthdeath > tools/microsatellite_birthdeath
• [ ] microsats_alignment_level > tools/microsats_alignment_level
• [ ] microsats_mutability > tools/microsats_mutability
• [ ] mine > tools/mine
• [ ] multispecies_orthologous_microsats > tools/multispecies_orthologous_microsats
• [ ] mutate_snp_codon > tools/mutate_snp_codon
• [ ] partialr_square > tools/partialr_square
• [ ] pearson_correlation > tools/pearson_correlation
• [ ] pgsnp2gd_snp > tools/pgsnp2gd_snp
• [ ] picard > tools/picard
• [x] pileup_interval > tool_collections/samtools/pileup_interval
• [ ] pileup_parser > tools/pileup_parser
• [ ] plot_from_lda > tools/plot_from_lda
• [ ] poisson2test > tool_collections/taxonomy/poisson2test
• [ ] principal_component_analysis > tools/principal_component_analysis
• [ ] print_reads > tool_collections/gatk/print_reads
• [ ] quality_filter > tools/quality_filter
• [ ] rcve > tools/rcve
• [ ] realigner_target_creator > tool_collections/gatk/realigner_target_creator
• [ ] remove_beginning > tools/remove_beginning
• [ ] rmap > tools/rmap
• [ ] rmapq > tools/rmapq
• [ ] sam2interval > tools/sam2interval
• [ ] sam_bitwise_flag_filter > tools/sam_bitwise_flag_filter
• [ ] sam_merge > tools/sam_merge
• [ ] sam_pileup > tools/sam_pileup
• [x] sam_to_bam > tool_collections/samtools/sam_to_bam
• [ ] samtool_filter2 > tools/samtool_filter2
• [x] samtools_flagstat > tool_collections/samtools/samtools_flagstat
• [x] samtools_mpileup > tool_collections/samtools/samtools_mpileup
• [x] samtools_phase > tool_collections/samtools/samtools_phase
• [x] samtools_rmdup > tool_collections/samtools/samtools_rmdup
• [x] samtools_slice_bam > tool_collections/samtools/samtools_slice_bam
• [ ] scatterplot > tools/scatterplot
• [ ] short_reads_figure_high_quality_length > tools/short_reads_figure_high_quality_length
• [ ] short_reads_figure_score > tools/short_reads_figure_score
• [ ] short_reads_trim_seq > tools/short_reads_trim_seq
• [ ] show_beginning > tools/show_beginning
• [ ] show_tail > tools/show_tail
• [ ] sicer > tools/sicer
• [ ] snpfreq > tool_collections/hgv/snpfreq
• [ ] split_paired_reads > tools/split_paired_reads
• [ ] substitution_rates > tools/substitution_rates
• [ ] substitutions > tools/substitutions
• [ ] subtract > tool_collections/gops/subtract
• [ ] subtract_query > tool_collections/gops/subtract_query
• [ ] t2ps > tool_collections/taxonomy/t2ps
• [ ] t2t_report > tool_collections/taxonomy/t2t_report
• [ ] table_annovar > tools/table_annovar
• [ ] table_recalibration > tool_collections/gatk/table_recalibration
• [ ] tables_arithmetic_operations > tool_collections/gops/tables_arithmetic_operations
• [ ] tabular_to_fasta > tools/tabular_to_fasta
• [ ] tabular_to_fastq > tool_collections/galaxy_sequence_utils/tabular_to_fastq
• [x] tophat > tools/tophat
• [x] tophat2 > tools/tophat2
• [ ] tophat_fusion_post > tools/tophat_fusion_post
• [ ] trimmer > tools/trimmer
• [ ] t_test_two_samples > tools/t_test_two_samples
• [ ] ucsc_custom_track > tools/ucsc_custom_track
• [ ] unified_genotyper > tool_collections/gatk/unified_genotyper
• [ ] variant_annotator > tool_collections/gatk/variant_annotator
• [ ] variant_apply_recalibration > tool_collections/gatk/variant_apply_recalibration
• [ ] variant_combine > tool_collections/gatk/variant_combine
• [ ] variant_eval > tool_collections/gatk/variant_eval
• [ ] variant_filtration > tool_collections/gatk/variant_filtration
• [ ] variant_recalibrator > tool_collections/gatk/variant_recalibrator
• [ ] variant_select > tool_collections/gatk/variant_select
• [ ] variants_validate > tool_collections/gatk/variants_validate
• [ ] varscan_version_2 > tools/varscan_version_2
• [ ] vcf2pgsnp > tools/vcf2pgsnp
• [ ] vcf_annotate > tools/vcf_annotate
• [ ] vcf_extract > tools/vcf_extract
• [ ] vcf_filter > tools/vcf_filter
• [ ] vcf_intersect > tools/vcf_intersect
• [ ] vcftools_annotate > tool_collections/vcftools/vcftools_annotate
• [ ] vcftools_compare > tool_collections/vcftools/vcftools_compare
• [ ] vcftools_isec > tool_collections/vcftools/vcftools_isec
• [ ] vcftools_merge > tool_collections/vcftools/vcftools_merge
• [ ] vcftools_slice > tool_collections/vcftools/vcftools_slice
• [ ] vcftools_subset > tool_collections/vcftools/vcftools_subset
• [ ] weblogo3 > tools/weblogo3
• [ ] weightedaverage > tools/weightedaverage
• [ ] windowsplitter > tools/windowsplitter
• [ ] xy_plot > tools/xy_plot

[bgruening]

Can we remove the old citations, or do we need to keep them for older Galaxy versions that do not support the citation tag?

[jmchilton]

Good question, I could go either way I guess. It has been two releases now I think it would be okay to start dropping citations in help where it makes sense. There may be places with the in-help citations add some context that is important though.

What do you think - you are the best practice guide author after all?

[bgruening]

I think we can start to drop it, on the other hand I know that I should care much more about backward compatibility. I will start this (slowly) ...

[peterjc]

I think older Galaxy installations would ignore the new citation tags - the only issue I remember hitting was with the ToolShed giving a "red message" on upload (long since fixed), see this thread http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-July/020090.html

[bgruening]

Peter; you are correct. But if I remove the old citations the user will not see any citation in older instances.

[peterjc]

For now I have been leaving citation information in the help text, duplicating it with the new XML markup.

I suppose at some point (once most Galaxy instances understand the citations tags) we can remove the free text citation information.

So I am +1 on adding XML citation tags now, but -1 on removing any plain text citation information in the existing tool help text.

[nsoranzo]

As Björn already knows, I agree with Peter that the old citation information should be preserved for some more time.

[bgruening]

@jmchilton do we have a citation for all the python/perl scripts that the Galaxy team has written?

[jmchilton]

@bgruening People should be citing Galaxy anyway so I am not sure - maybe someone who has been around longer has an opinion.

[blankenberg]

The Galaxy citation would have to be determined on a case-by-case basis, if e.g. a Galaxy tool was developed/wrapped for/appeared in a particular Galaxy-associated paper, then that paper should be included as a citation -- hopefully where the Galaxy tool script/wrapper coder is an author.

Some quick examples include most MAF and FASTQ tools.