# HG changeset patch # User iuc # Date 1533732579 14400 # Node ID 1c2db0054039527f042f9fff271256d888a66d7e # Parent f0ec41881020ff46f8426c076301d465dc75c91b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984 diff -r f0ec41881020 -r 1c2db0054039 multiqc.xml --- a/multiqc.xml Mon Aug 06 10:42:11 2018 -0400 +++ b/multiqc.xml Wed Aug 08 08:49:39 2018 -0400 @@ -1,7 +1,7 @@ - + aggregate results from bioinformatics analyses into a single report - 1.5 + 1.6 deepTools + @@ -584,6 +593,9 @@ + + + @@ -813,6 +825,12 @@ + + + + + + @@ -846,6 +864,7 @@ + @@ -855,6 +874,7 @@ + diff -r f0ec41881020 -r 1c2db0054039 test-data/aligner_soft_stats.tabular --- a/test-data/aligner_soft_stats.tabular Mon Aug 06 10:42:11 2018 -0400 +++ b/test-data/aligner_soft_stats.tabular Wed Aug 08 08:49:39 2018 -0400 @@ -1,4 +1,4 @@ -Sample Cutadapt_mqc-generalstats-percent_trimmed Kallisto_mqc-generalstats-fragment_length Kallisto_mqc-generalstats-percent_aligned Kallisto_mqc-generalstats-pseudoaligned_reads Bismark_mqc-generalstats-aligned_reads Bismark_mqc-generalstats-percent_aligned Bowtie 2_mqc-generalstats-overall_alignment_rate HiCExplorer_mqc-generalstats-Pairs_considered HiCExplorer_mqc-generalstats-Pairs_used HiCExplorer_mqc-generalstats-Mapped HiCExplorer_mqc-generalstats-Min_rest_site_distance HiCExplorer_mqc-generalstats-Max_rest_site_distance HISAT2_mqc-generalstats-overall_alignment_rate STAR_mqc-generalstats-uniquely_mapped_percent STAR_mqc-generalstats-uniquely_mapped Tophat_mqc-generalstats-overall_aligned_percent Tophat_mqc-generalstats-aligned_not_multimapped_discordant MACS2_mqc-generalstats-d MACS2_mqc-generalstats-treatment_redundant_rate MACS2_mqc-generalstats-control_redundant_rate +Sample Cutadapt_mqc-generalstats-cutadapt-percent_trimmed Kallisto_mqc-generalstats-kallisto-fragment_length Kallisto_mqc-generalstats-kallisto-percent_aligned Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads Bismark_mqc-generalstats-bismark-aligned_reads Bismark_mqc-generalstats-bismark-percent_aligned Bowtie 2_mqc-generalstats-bowtie_2-overall_alignment_rate HiCExplorer_mqc-generalstats-hicexplorer-Pairs_considered HiCExplorer_mqc-generalstats-hicexplorer-Pairs_used HiCExplorer_mqc-generalstats-hicexplorer-Mapped HiCExplorer_mqc-generalstats-hicexplorer-Min_rest_site_distance HiCExplorer_mqc-generalstats-hicexplorer-Max_rest_site_distance HISAT2_mqc-generalstats-hisat2-overall_alignment_rate STAR_mqc-generalstats-star-uniquely_mapped_percent STAR_mqc-generalstats-star-uniquely_mapped Tophat_mqc-generalstats-tophat-overall_aligned_percent Tophat_mqc-generalstats-tophat-aligned_not_multimapped_discordant MACS2_mqc-generalstats-macs2-d MACS2_mqc-generalstats-macs2-treatment_redundant_rate MACS2_mqc-generalstats-macs2-control_redundant_rate HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1 5.880883098970165 HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1 167.866 83.65114569077758 48531088.0 HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2 31.038195169381073 diff -r f0ec41881020 -r 1c2db0054039 test-data/fastp1.json.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastp1.json.txt Wed Aug 08 08:49:39 2018 -0400 @@ -0,0 +1,217 @@ +{ + "summary": { + "before_filtering": { + "total_reads":2, + "total_bases":302, + "q20_bases":262, + "q30_bases":241, + "q20_rate":0.86755, + "q30_rate":0.798013, + "read1_mean_length":151, + "gc_content":0.36755 + }, + "after_filtering": { + "total_reads":2, + "total_bases":286, + "q20_bases":246, + "q30_bases":226, + "q20_rate":0.86014, + "q30_rate":0.79021, + "read1_mean_length":143, + "gc_content":0.367133 + } + }, + "filtering_result": { + "passed_filter_reads": 2, + "low_quality_reads": 0, + "too_many_N_reads": 0, + "too_short_reads": 0, + "too_long_reads": 0 + }, + "duplication": { + "rate": 0, + "histogram": 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"q30_rate":0.907789, + "read1_mean_length":236, + "read2_mean_length":236, + "gc_content":0.479928 + } + }, + "filtering_result": { + "passed_filter_reads": 194, + "low_quality_reads": 2, + "too_many_N_reads": 2, + "too_short_reads": 0, + "too_long_reads": 0 + }, + "duplication": { + "rate": 0, + "histogram": [69,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0], + "mean_gc": [0.396022,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0] + }, + "insert_size": { + "peak": 308, + "unknown": 4, + "histogram": 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"fastp --thread 1 --report_title fastp report for bwa-mem-fastq1_fq.fastq -i bwa-mem-fastq1_fq.fastq -o first.fastq -I bwa-mem-fastq2_fq.fastq -O second.fastq " +} \ No newline at end of file diff -r f0ec41881020 -r 1c2db0054039 test-data/fastp_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastp_stats.tabular Wed Aug 08 08:49:39 2018 -0400 @@ -0,0 +1,3 @@ +Sample command +R1_fq fastp --thread 1 --report_title fastp report for R1_fq.fastq -i R1_fq.fastq -o first.fastq -U --umi_loc read1 --umi_len 8 +bwa-mem-fastq1_fq fastp --thread 1 --report_title fastp report for bwa-mem-fastq1_fq.fastq -i bwa-mem-fastq1_fq.fastq -o first.fastq -I bwa-mem-fastq2_fq.fastq -O second.fastq diff -r f0ec41881020 -r 1c2db0054039 test-data/post_aligner_soft_stats.tabular --- a/test-data/post_aligner_soft_stats.tabular Mon Aug 06 10:42:11 2018 -0400 +++ b/test-data/post_aligner_soft_stats.tabular Wed Aug 08 08:49:39 2018 -0400 @@ -1,22 +1,22 @@ -Sample QUAST_mqc-generalstats-N50 QUAST_mqc-generalstats-Total_length featureCounts_mqc-generalstats-percent_assigned featureCounts_mqc-generalstats-Assigned Picard_mqc-generalstats-PCT_PF_READS_ALIGNED Prokka_mqc-generalstats-contigs Prokka_mqc-generalstats-organism Prokka_mqc-generalstats-bases Prokka_mqc-generalstats-CDS Bcftools Stats_mqc-generalstats-tstv Bcftools Stats_mqc-generalstats-number_of_MNPs Bcftools Stats_mqc-generalstats-number_of_indels Bcftools Stats_mqc-generalstats-number_of_SNPs Bcftools Stats_mqc-generalstats-number_of_records Bamtools_mqc-generalstats-duplicates_pct Bamtools_mqc-generalstats-mapped_reads_pct Picard_mqc-generalstats-PERCENT_DUPLICATION Picard_mqc-generalstats-summed_median Picard_mqc-generalstats-summed_mean GATK VariantEval_mqc-generalstats-known_titv GATK VariantEval_mqc-generalstats-novel_titv HTSeq Count_mqc-generalstats-percent_assigned HTSeq Count_mqc-generalstats-assigned Picard_mqc-generalstats-PCT_MRNA_BASES Picard_mqc-generalstats-PCT_RIBOSOMAL_BASES Samtools Flagstat_mqc-generalstats-mapped_passed Samtools Stats_mqc-generalstats-raw_total_sequences Samtools Stats_mqc-generalstats-non_primary_alignments Samtools Stats_mqc-generalstats-reads_mapped Samtools Stats_mqc-generalstats-error_rate Samtools Stats_mqc-generalstats-reads_mapped_percent SnpEff_mqc-generalstats-Ts_Tv_ratio SnpEff_mqc-generalstats-Number_of_variants_before_filter SnpEff_mqc-generalstats-Change_rate Samblaster_mqc-generalstats-pct_dups -14892_1#15 115136.0 18435361.0 -70: TopHat on data 1, data 4, and data 3: accepted_hits 70.82267755353567 321797 -75: TopHat on data 1, data 6, and data 5: accepted_hits 69.58585803304067 445012 -80: TopHat on data 1, data 8, and data 7: accepted_hits 71.76957768385707 394981 -85: TopHat on data 1, data 10, and data 9: accepted_hits 72.02454351337069 437485 -90: TopHat on data 1, data 12, and data 11: accepted_hits 71.33130826437625 388170 -95: TopHat on data 1, data 14, and data 13: accepted_hits 70.72517103678439 453929 -D11_H4K16ac_Rep1_R1_fastq_gz 0.983085 -Sample1 30 Helicobacter pylori 1629978 1548 -Sample2 52 Escherichia coli 162997532523 1548 -Test1 1.97 72330.0 902934.0 4474244.0 5522770.0 -bamtools 0.0 93.125 -dataset_114 0.005582 -dataset_197 176 271.809759 -gatk_varianteval 0.0 2.2 -htseq 0.0 0 -picard_CollectRnaSeqMetrics_bam 79.62310000000001 -samtools_flagstat 20689039 -samtools_stats 641821.0 12111.0 641821.0 0.004248509 100.0 -snpeff 0.0 972155.0 3190.0 -virtual-normal 1.28 +Sample QUAST_mqc-generalstats-quast-N50 QUAST_mqc-generalstats-quast-Total_length featureCounts_mqc-generalstats-featurecounts-percent_assigned featureCounts_mqc-generalstats-featurecounts-Assigned Picard_mqc-generalstats-picard-PCT_PF_READS_ALIGNED Prokka_mqc-generalstats-prokka-organism Prokka_mqc-generalstats-prokka-contigs Prokka_mqc-generalstats-prokka-bases Prokka_mqc-generalstats-prokka-CDS Bcftools Stats_mqc-generalstats-bcftools_stats-number_of_records Bcftools Stats_mqc-generalstats-bcftools_stats-number_of_SNPs Bcftools Stats_mqc-generalstats-bcftools_stats-number_of_indels Bcftools Stats_mqc-generalstats-bcftools_stats-tstv Bcftools Stats_mqc-generalstats-bcftools_stats-number_of_MNPs Bamtools_mqc-generalstats-bamtools-duplicates_pct Bamtools_mqc-generalstats-bamtools-mapped_reads_pct Picard_mqc-generalstats-picard-PERCENT_DUPLICATION Picard_mqc-generalstats-picard-summed_median Picard_mqc-generalstats-picard-summed_mean GATK VariantEval_mqc-generalstats-gatk_varianteval-known_titv GATK VariantEval_mqc-generalstats-gatk_varianteval-novel_titv HTSeq Count_mqc-generalstats-htseq_count-percent_assigned HTSeq Count_mqc-generalstats-htseq_count-assigned Picard_mqc-generalstats-picard-PCT_RIBOSOMAL_BASES Picard_mqc-generalstats-picard-PCT_MRNA_BASES Samtools Flagstat_mqc-generalstats-samtools_flagstat-mapped_passed Samtools Stats_mqc-generalstats-samtools_stats-error_rate Samtools Stats_mqc-generalstats-samtools_stats-non_primary_alignments Samtools Stats_mqc-generalstats-samtools_stats-reads_mapped Samtools Stats_mqc-generalstats-samtools_stats-reads_mapped_percent Samtools Stats_mqc-generalstats-samtools_stats-reads_properly_paired_percent Samtools Stats_mqc-generalstats-samtools_stats-reads_MQ0_percent Samtools Stats_mqc-generalstats-samtools_stats-raw_total_sequences SnpEff_mqc-generalstats-snpeff-Change_rate SnpEff_mqc-generalstats-snpeff-Ts_Tv_ratio SnpEff_mqc-generalstats-snpeff-Number_of_variants_before_filter Samblaster_mqc-generalstats-samblaster-pct_dups +14892_1#15 115136.0 18435361.0 +70: TopHat on data 1, data 4, and data 3: accepted_hits 70.82267755353567 321797 +75: TopHat on data 1, data 6, and data 5: accepted_hits 69.58585803304067 445012 +80: TopHat on data 1, data 8, and data 7: accepted_hits 71.76957768385707 394981 +85: TopHat on data 1, data 10, and data 9: accepted_hits 72.02454351337069 437485 +90: TopHat on data 1, data 12, and data 11: accepted_hits 71.33130826437625 388170 +95: TopHat on data 1, data 14, and data 13: accepted_hits 70.72517103678439 453929 +D11_H4K16ac_Rep1_R1_fastq_gz 0.983085 +Sample1 Helicobacter pylori 30 1629978 1548 +Sample2 Escherichia coli 52 162997532523 1548 +Test1 5522770.0 4474244.0 902934.0 1.97 72330.0 +bamtools_txt 0.0 93.125 +dataset_114 0.005582 +dataset_197 176 271.809759 +gatk_varianteval_txt 0.0 2.2 +htseq_txt 0.0 0 +picard_CollectRnaSeqMetrics_bam 79.62310000000001 +samtools_flagstat_txt 20689039 +samtools_stats_txt 0.004248509 12111.0 641821.0 100.0 99.03477760933345 0.010906467691147531 641821.0 +snpeff_csv 3190.0 0.0 972155.0 +virtual-normal 1.28 diff -r f0ec41881020 -r 1c2db0054039 test-data/pre_alignment_soft_stats.tabular --- a/test-data/pre_alignment_soft_stats.tabular Mon Aug 06 10:42:11 2018 -0400 +++ b/test-data/pre_alignment_soft_stats.tabular Wed Aug 08 08:49:39 2018 -0400 @@ -1,7 +1,9 @@ -Sample SortMeRNA_mqc-generalstats-rRNA_pct Trimmomatic_mqc-generalstats-dropped_pct Cutadapt_mqc-generalstats-percent_trimmed FastQC_mqc-generalstats-avg_sequence_length FastQC_mqc-generalstats-percent_fails FastQC_mqc-generalstats-percent_duplicates FastQC_mqc-generalstats-percent_gc FastQC_mqc-generalstats-total_sequences Flexbar_mqc-generalstats-removed_bases_pct -25839_merged 1.099299750020029 -C2 17.98 -dataset_33 10.776820436239396 -poulet5_1 101.0 8.333333333333332 36.30591159931017 48.0 267849.0 -poulet5_2 101.0 8.333333333333332 36.173388748054116 48.0 267849.0 -result_right 45.26066350710901 +Sample SortMeRNA_mqc-generalstats-sortmerna-rRNA_pct Trimmomatic_mqc-generalstats-trimmomatic-dropped_pct fastp_mqc-generalstats-fastp-pct_duplication fastp_mqc-generalstats-fastp-after_filtering_q30_rate fastp_mqc-generalstats-fastp-after_filtering_q30_bases fastp_mqc-generalstats-fastp-after_filtering_gc_content fastp_mqc-generalstats-fastp-pct_surviving fastp_mqc-generalstats-fastp-pct_adapter Cutadapt_mqc-generalstats-cutadapt-percent_trimmed FastQC_mqc-generalstats-fastqc-percent_duplicates FastQC_mqc-generalstats-fastqc-percent_gc FastQC_mqc-generalstats-fastqc-avg_sequence_length FastQC_mqc-generalstats-fastqc-percent_fails FastQC_mqc-generalstats-fastqc-total_sequences Flexbar_mqc-generalstats-flexbar-removed_bases_pct +25839_merged 1.099299750020029 +C2 17.98 +R1_fq 0.0 0.79021 226.0 0.367133 100.0 +bwa-mem-fastq1_fq 0.0 0.907789 41653.0 0.479928 97.97979797979798 33.33333333333333 +dataset_33 10.776820436239396 +poulet5_1 36.30591159931017 48.0 101.0 8.333333333333332 267849.0 +poulet5_2 36.173388748054116 48.0 101.0 8.333333333333332 267849.0 +result_right 45.26066350710901