# HG changeset patch # User iuc # Date 1524657592 14400 # Node ID df99138d277636ea810834d32780ea97091d86e6 # Parent e0f4a651c6b90776f97c29696b2bcc4d65727e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 31d721c19f5681dfe542dd23185c06c8f29f1945 diff -r e0f4a651c6b9 -r df99138d2776 generate_test_data.sh --- a/generate_test_data.sh Fri Apr 20 01:06:25 2018 -0400 +++ b/generate_test_data.sh Wed Apr 25 07:59:52 2018 -0400 @@ -46,8 +46,9 @@ cp 'test-data/hisat2_2.txt' 'multiqc_WDir/hisat2/hisat2_2.txt' mkdir -p 'multiqc_WDir/hicexplorer' -cp 'test-data/hicexplorer1.log' 'multiqc_WDir/hicexplorer/' -cp 'test-data/hicexplorer2.log' 'multiqc_WDir/hicexplorer/' +cp 'test-data/hicexplorer1.log' 'multiqc_WDir/hicexplorer/hicexplorer1' +cp 'test-data/hicexplorer1.log' 'multiqc_WDir/hicexplorer/hicexplorer1_1' +cp 'test-data/hicexplorer2.log' 'multiqc_WDir/hicexplorer/hicexplorer2' mkdir -p 'multiqc_WDir/kallisto' cp 'test-data/kallisto_1.txt' 'multiqc_WDir/kallisto/kallisto_1.txt' diff -r e0f4a651c6b9 -r df99138d2776 multiqc.xml --- a/multiqc.xml Fri Apr 20 01:06:25 2018 -0400 +++ b/multiqc.xml Wed Apr 25 07:59:52 2018 -0400 @@ -8,6 +8,10 @@ ]]> @@ -23,6 +27,7 @@ ]]> - + @@ -910,7 +917,7 @@ - + diff -r e0f4a651c6b9 -r df99138d2776 test-data/aligner_soft_report.html --- a/test-data/aligner_soft_report.html Fri Apr 20 01:06:25 2018 -0400 +++ b/test-data/aligner_soft_report.html Wed Apr 25 07:59:52 2018 -0400 @@ -24,7 +24,7 @@ @@ -4746,7 +4746,7 @@

Report generated on 2018-04-06, 16:47 based on data in: +

Report generated on 2018-04-23, 22:00 based on data in: /Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_WDir

@@ -4788,12 +4788,12 @@ Plot - Showing ¹⁵/₁₅ rows and ¹⁴/₁₅ columns. + Showing ¹⁶/₁₆ rows and ¹⁴/₁₅ columns.

Sample Name	M Aligned	% Aligned	M Pairs	% Used pairs	% Mapped	Min RE dist	Max RE dist	Frag Length	M Aligned	% Aligned	M Aligned	% Aligned	% Aligned	M Aligned	% Trimmed
HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1															5.9%
HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1		83.7%						167.9bp	48.5
HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2															31.0%
HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1															7.7%
HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1		84.5%						169.4bp	59.3
HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2															32.2%
bismark_SE_report	0.2	69.7%
bowtie2_1												98.3%
bowtie2_2												98.3%
hicexplorer_hicexplorer1_small_test			0.1	37.3%	91.2%	303 bp	800 bp
hicexplorer_hicexplorer2_small_test_rf			0.1	35.9%	91.2%	152 bp	1500 bp
hisat2_1												96.2%
hisat2_2												96.2%
star_log										89.0%	0.0
tophat_align													99.5%	0.3

+ Sample NameHS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1

5.9%

HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1

83.7%

167.9bp

48.5

HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2

31.0%

HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1

7.7%

HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1

84.5%

169.4bp

59.3

HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2

32.2%

bismark_SE_report

0.2

69.7%

bowtie2_1

98.3%

bowtie2_2

98.3%

hicexplorer_hicexplorer1_1_small_test

0.1

37.3%

91.2%

303 bp

800 bp

hicexplorer_hicexplorer1_small_test

0.1

37.3%

91.2%

303 bp

800 bp

hicexplorer_hicexplorer2_small_test_rf

0.1

35.9%

91.2%

152 bp

1500 bp

hisat2_1

96.2%

hisat2_2

96.2%

star_log

89.0%

0.0

tophat_align

99.5%

0.3

diff -r e0f4a651c6b9 -r df99138d2776 test-data/aligner_soft_stats.tabular --- a/test-data/aligner_soft_stats.tabular Fri Apr 20 01:06:25 2018 -0400 +++ b/test-data/aligner_soft_stats.tabular Wed Apr 25 07:59:52 2018 -0400 @@ -1,16 +1,17 @@ -Sample Cutadapt_mqc-generalstats-percent_trimmed Kallisto_mqc-generalstats-pseudoaligned_reads Kallisto_mqc-generalstats-fragment_length Kallisto_mqc-generalstats-percent_aligned Bismark_mqc-generalstats-aligned_reads Bismark_mqc-generalstats-percent_aligned Bowtie 2_mqc-generalstats-overall_alignment_rate HiCExplorer_mqc-generalstats-Mapped HiCExplorer_mqc-generalstats-Pairs_used HiCExplorer_mqc-generalstats-Min_rest_site_distance HiCExplorer_mqc-generalstats-Pairs_considered 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 +Sample Cutadapt_mqc-generalstats-percent_trimmed Kallisto_mqc-generalstats-percent_aligned Kallisto_mqc-generalstats-fragment_length Kallisto_mqc-generalstats-pseudoaligned_reads Bismark_mqc-generalstats-percent_aligned Bismark_mqc-generalstats-aligned_reads Bowtie 2_mqc-generalstats-overall_alignment_rate HiCExplorer_mqc-generalstats-Pairs_used HiCExplorer_mqc-generalstats-Min_rest_site_distance HiCExplorer_mqc-generalstats-Mapped HiCExplorer_mqc-generalstats-Max_rest_site_distance HiCExplorer_mqc-generalstats-Pairs_considered HISAT2_mqc-generalstats-overall_alignment_rate STAR_mqc-generalstats-uniquely_mapped STAR_mqc-generalstats-uniquely_mapped_percent Tophat_mqc-generalstats-aligned_not_multimapped_discordant Tophat_mqc-generalstats-overall_aligned_percent HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1 5.880883098970165 -HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1 48531088.0 167.866 83.65114569077758 +HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1 83.65114569077758 167.866 48531088.0 HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2 31.038195169381073 HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1 7.7267901650356645 -HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1 59280920.0 169.418 84.50278473550448 +HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1 84.50278473550448 169.418 59280920.0 HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2 32.18485266309055 -bismark_SE_report 220558.0 69.71079996207212 +bismark_SE_report 69.71079996207212 220558.0 bowtie2_1 98.33 bowtie2_2 98.31 -hicexplorer_hicexplorer1_small_test 0.08778492343698428 0.3732734564876029 303.0 99983.0 800.0 -hicexplorer_hicexplorer2_small_test_rf 0.08778492343698428 0.35940109818669175 152.0 99983.0 1500.0 +hicexplorer_hicexplorer1_1_small_test 0.3732734564876029 303.0 0.08778492343698428 800.0 99983.0 +hicexplorer_hicexplorer1_small_test 0.3732734564876029 303.0 0.08778492343698428 800.0 99983.0 +hicexplorer_hicexplorer2_small_test_rf 0.35940109818669175 152.0 0.08778492343698428 1500.0 99983.0 hisat2_1 96.15 hisat2_2 96.15 star_log 89.0 89.0 -tophat_align 99.5 307733.0 +tophat_align 307733.0 99.5 diff -r e0f4a651c6b9 -r df99138d2776 test-data/bowtie2_stats.tabular --- a/test-data/bowtie2_stats.tabular Fri Apr 20 01:06:25 2018 -0400 +++ b/test-data/bowtie2_stats.tabular Wed Apr 25 07:59:52 2018 -0400 @@ -1,3 +1,3 @@ -Sample unpaired_total unpaired_aligned_multi overall_alignment_rate unpaired_aligned_none total_reads unpaired_aligned_one -bowtie2_1 21040602 7389576 98.33 351563 21040602 13299463 -bowtie2_2 16199126 5837404 98.31 274008 16199126 10087714 +Sample unpaired_total total_reads unpaired_aligned_one unpaired_aligned_none overall_alignment_rate unpaired_aligned_multi +bowtie2_1 21040602 21040602 13299463 351563 98.33 7389576 +bowtie2_2 16199126 16199126 10087714 274008 98.31 5837404 diff -r e0f4a651c6b9 -r df99138d2776 test-data/hisat2_stats.tabular --- a/test-data/hisat2_stats.tabular Fri Apr 20 01:06:25 2018 -0400 +++ b/test-data/hisat2_stats.tabular Wed Apr 25 07:59:52 2018 -0400 @@ -1,3 +1,3 @@ -Sample unpaired_aligned_multi overall_alignment_rate unpaired_aligned_none unpaired_total unpaired_aligned_one -hisat2_1 9953 96.15 3849 99978 86176 -hisat2_2 9953 96.15 3849 99978 86176 +Sample unpaired_total overall_alignment_rate unpaired_aligned_one unpaired_aligned_none unpaired_aligned_multi +hisat2_1 99978 96.15 86176 3849 9953 +hisat2_2 99978 96.15 86176 3849 9953 diff -r e0f4a651c6b9 -r df99138d2776 test-data/kallisto_stats.tabular --- a/test-data/kallisto_stats.tabular Fri Apr 20 01:06:25 2018 -0400 +++ b/test-data/kallisto_stats.tabular Wed Apr 25 07:59:52 2018 -0400 @@ -1,3 +1,3 @@ -Sample pseudoaligned_reads not_pseudoaligned_reads total_reads percent_aligned fragment_length -HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1 48531088.0 9484959.0 58016047.0 83.65114569077758 167.866 -HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1 59280920.0 10871703.0 70152623.0 84.50278473550448 169.418 +Sample percent_aligned total_reads not_pseudoaligned_reads pseudoaligned_reads fragment_length +HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1 83.65114569077758 58016047.0 9484959.0 48531088.0 167.866 +HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1 84.50278473550448 70152623.0 10871703.0 59280920.0 169.418 diff -r e0f4a651c6b9 -r df99138d2776 test-data/star_stats.tabular --- a/test-data/star_stats.tabular Fri Apr 20 01:06:25 2018 -0400 +++ b/test-data/star_stats.tabular Wed Apr 25 07:59:52 2018 -0400 @@ -1,2 +1,2 @@ -Sample multimapped_percent insertion_rate multimapped_toomany_percent num_annotated_splices num_GTAG_splices uniquely_mapped unmapped_tooshort_percent deletion_length mismatch_rate insertion_length num_noncanonical_splices num_ATAC_splices deletion_rate multimapped_toomany total_reads num_GCAG_splices num_splices unmapped_mismatches_percent unmapped_other_percent unmapped_mismatches unmapped_tooshort multimapped unmapped_other avg_mapped_read_length uniquely_mapped_percent avg_input_read_length -star_log 1.0 0.0 0.0 0.0 47.0 89.0 10.0 0.0 1.73 0.0 0.0 0.0 0.0 0.0 100.0 0.0 47.0 0.0 0.0 0 10 1.0 0 74.8 89.0 75.0 +Sample mismatch_rate avg_input_read_length num_annotated_splices multimapped_toomany_percent num_splices uniquely_mapped uniquely_mapped_percent multimapped multimapped_toomany unmapped_tooshort multimapped_percent num_ATAC_splices unmapped_tooshort_percent total_reads unmapped_mismatches num_noncanonical_splices insertion_rate unmapped_other_percent num_GTAG_splices insertion_length deletion_length deletion_rate unmapped_other unmapped_mismatches_percent num_GCAG_splices avg_mapped_read_length +star_log 1.73 75.0 0.0 0.0 47.0 89.0 89.0 1.0 0.0 10 1.0 0.0 10.0 100.0 0 0.0 0.0 0.0 47.0 0.0 0.0 0.0 0 0.0 0.0 74.8 diff -r e0f4a651c6b9 -r df99138d2776 test-data/tophat_stats.tabular --- a/test-data/tophat_stats.tabular Fri Apr 20 01:06:25 2018 -0400 +++ b/test-data/tophat_stats.tabular Wed Apr 25 07:59:52 2018 -0400 @@ -1,2 +1,2 @@ -Sample aligned_not_multimapped_discordant concordant_aligned_percent unaligned_total aligned_total aligned_multimap total_reads aligned_discordant overall_aligned_percent -tophat_align 307733.0 99.0 2985.0 313405.0 5638.0 316390.0 34.0 99.5 +Sample total_reads concordant_aligned_percent unaligned_total aligned_total aligned_multimap aligned_discordant overall_aligned_percent aligned_not_multimapped_discordant +tophat_align 316390.0 99.0 2985.0 313405.0 5638.0 34.0 99.5 307733.0