Add citations to all the tools.

- [ ] 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