| Previous changeset 10:ce0f144f4835 (2018-08-05) Next changeset 12:1c2db0054039 (2018-08-08) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23 |
|
modified:
multiqc.xml test-data/aligner_soft_stats.tabular |
|
added:
test-data/macs_1.txt test-data/macs_2.txt test-data/macs_stats.tabular |
| b |
| diff -r ce0f144f4835 -r f0ec41881020 multiqc.xml --- a/multiqc.xml Sun Aug 05 18:26:28 2018 -0400 +++ b/multiqc.xml Mon Aug 06 10:42:11 2018 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.1"> +<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.2"> <description>aggregate results from bioinformatics analyses into a single report</description> <macros> <token name="@WRAPPER_VERSION@">1.5</token> @@ -216,6 +216,14 @@ #elif str($repeat.software_cond.software) == "kallisto" #set $pattern = "finding pseudoalignments for the reads" @LN_FILES@ + #elif str($repeat.software_cond.software) == "macs2" + #set $pattern = "# This file is generated by MACS" + #for $file in $repeat.software_cond.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($software_dir, str($identifier) + '_peaks.xls') + grep -q "$pattern" $file || die "'$pattern' not found in the file" && + ln -s '$file' '$file_path' && + #end for #elif str($repeat.software_cond.software) == "picard" #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) #if str($repeat2.type) == "alignment_metrics" @@ -505,7 +513,7 @@ <!--<option value="jellyfish">Jellyfish</option>--> <option value="kallisto">Kallisto</option> <!--<option value="leehom">leeHom</option>--> - <!--<option value="macs2">MACS2</option>--> + <option value="macs2">MACS2</option> <!--<option value="methylQA">methylQA</option>--> <!--<option value="peddy">Peddy</option>--> <option value="picard">Picard</option> @@ -614,6 +622,9 @@ <when value="kallisto"> <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Kallisto" help="It should contain '[quant] finding pseudoalignments for the reads'"/> </when> + <when value="macs2"> + <param name="input" type="data" format="txt,tabular,tsv" multiple="true" label="Output of MACS2" help="It should be a tabular file containing '# This file is generated by MACS'"/> + </when> <when value="picard"> <repeat name="output" title="Picard output" min="1"> <param name="type" type="select" label="Type of Picard output?"> @@ -887,6 +898,12 @@ </repeat> <repeat name="results"> <conditional name="software_cond"> + <param name="software" value="macs2" /> + <param name="input" value="macs_1.txt,macs_2.txt" /> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> <param name="software" value="star" /> <repeat name="output"> <conditional name="type"> @@ -915,6 +932,7 @@ <has_text text="bowtie2_se_plot" /> <has_text text="hisat2_se_plot" /> <has_text text="kallisto_alignment" /> + <has_text text="MACS2" /> <has_text text="star_alignment_plot" /> <has_text text="tophat_alignment" /> <has_text text="hicexplorer" /> @@ -928,6 +946,7 @@ <element name="hisat2" file="hisat2_stats.tabular" compare="sim_size" delta="20"/> <!-- <element name="hicexplorer" file="hicexplorer_stats.tabular" compare="sim_size" delta="0"/> --> <element name="kallisto" file="kallisto_stats.tabular" compare="sim_size" delta="10"/> + <element name="macs" file="macs_stats.tabular" compare="sim_size" delta="10"/> <element name="star" file="star_stats.tabular" compare="sim_size" delta="10"/> <element name="tophat.txt" file="tophat_stats.tabular" compare="sim_size" delta="10"/> </output_collection> |
| b |
| diff -r ce0f144f4835 -r f0ec41881020 test-data/aligner_soft_stats.tabular --- a/test-data/aligner_soft_stats.tabular Sun Aug 05 18:26:28 2018 -0400 +++ b/test-data/aligner_soft_stats.tabular Mon Aug 06 10:42:11 2018 -0400 |
| b |
| @@ -1,17 +1,19 @@ -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 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 84.50278473550448 169.418 59280920.0 -HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2 32.18485266309055 -bismark_SE_report 69.71079996207212 220558.0 -bowtie2_1 98.33 -bowtie2_2 98.31 -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 307733.0 99.5 +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 +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 +HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1 7.7267901650356645 +HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1 169.418 84.50278473550448 59280920.0 +HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2 32.18485266309055 +bismark_txt_SE_report 220558.0 69.71079996207212 +bowtie2_1_txt 98.33 +bowtie2_2_txt 98.31 +hicexplorer_3_hicexplorer1_log_1_small_test 99983.0 0.3732734564876029 0.08778492343698428 303.0 800.0 +hicexplorer_3_hicexplorer1_log_small_test 99983.0 0.3732734564876029 0.08778492343698428 303.0 800.0 +hicexplorer_3_hicexplorer2_log_small_test_rf 99983.0 0.35940109818669175 0.08778492343698428 152.0 1500.0 +hisat2_1_txt 96.15 +hisat2_2_txt 96.15 +star_log_txt 89.0 89.0 +tophat_txtalign 99.5 307733.0 +treat1 254.0 0.0 0.0 +treat2 254.0 0.0 0.0 |
| b |
| diff -r ce0f144f4835 -r f0ec41881020 test-data/macs_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/macs_1.txt Mon Aug 06 10:42:11 2018 -0400 |
| [ |
| @@ -0,0 +1,100 @@ +# This file is generated by MACS version 2.1.1.20160309 +# Command line: callpeak --name treat1 -t /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpiNVEd5/files/000/dataset_1.dat -c /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpiNVEd5/files/000/dataset_2.dat --format BED --gsize 2700000000 --keep-dup 1 --qvalue 0.05 --mfold 5 50 --bw 300 +# ARGUMENTS LIST: +# name = treat1 +# format = BED +# ChIP-seq file = ['/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpiNVEd5/files/000/dataset_1.dat'] +# control file = ['/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpiNVEd5/files/000/dataset_2.dat'] +# effective genome size = 2.70e+09 +# band width = 300 +# model fold = [5, 50] +# qvalue cutoff = 5.00e-02 +# Larger dataset will be scaled towards smaller dataset. +# Range for calculating regional lambda is: 1000 bps and 10000 bps +# Broad region calling is off +# Paired-End mode is off + +# tag size is determined as 100 bps +# total tags in treatment: 199977 +# tags after filtering in treatment: 199583 +# maximum duplicate tags at the same position in treatment = 1 +# Redundant rate in treatment: 0.00 +# total tags in control: 199978 +# tags after filtering in control: 199867 +# maximum duplicate tags at the same position in control = 1 +# Redundant rate in control: 0.00 +# d = 254 +# alternative fragment length(s) may be 254 bps +chr start end length abs_summit pileup -log10(pvalue) fold_enrichment -log10(qvalue) name +chr1 840082 840400 319 840240 4.00 10.71801 4.90785 7.08620 MACS2_peak_1 +chr1 919420 919785 366 919550 5.00 12.44148 5.85158 8.70936 MACS2_peak_2 +chr1 937221 937483 263 937375 4.00 10.06728 4.87632 6.61759 MACS2_peak_3 +chr1 954743 954996 254 954814 3.00 8.29236 3.92628 4.97243 MACS2_peak_4 +chr1 994763 995016 254 994906 3.00 8.29236 3.92628 4.97243 MACS2_peak_5 +chr1 1057395 1057648 254 1057509 3.00 8.29236 3.92628 4.97243 MACS2_peak_6 +chr1 1240580 1241004 425 1240777 3.00 7.77216 3.90105 4.60940 MACS2_peak_7 +chr1 1307393 1307735 343 1307601 5.00 12.44148 5.85158 8.70936 MACS2_peak_8 +chr1 1440351 1440633 283 1440462 4.00 10.71801 4.90785 7.08620 MACS2_peak_9 +chr1 1555433 1555725 293 1555571 4.00 10.71801 4.90785 7.08620 MACS2_peak_10 +chr1 1590668 1590946 279 1590840 4.00 10.06728 4.87632 6.61759 MACS2_peak_11 +chr1 1837669 1838104 436 1837886 6.00 14.88256 6.82684 10.84922 MACS2_peak_12 +chr1 1840366 1840828 463 1840547 5.00 13.22276 5.88942 9.29290 MACS2_peak_13 +chr1 1976400 1976653 254 1976469 3.00 8.29236 3.92628 4.97243 MACS2_peak_14 +chr1 2071302 2071627 326 2071423 4.00 10.71801 4.90785 7.08620 MACS2_peak_15 +chr1 2105717 2106140 424 2105919 4.00 7.70001 4.64644 4.60940 MACS2_peak_16 +chr1 2126522 2126861 340 2126648 4.00 10.06728 4.87632 6.61759 MACS2_peak_17 +chr1 2246521 2246954 434 2246712 5.00 9.59761 5.57573 6.23289 MACS2_peak_18 +chr1 2313158 2313560 403 2313353 5.00 13.22276 5.88942 9.29290 MACS2_peak_19 +chr1 2345828 2346242 415 2346028 7.00 17.38158 7.80211 13.02598 MACS2_peak_20 +chr1 2510055 2510308 254 2510213 3.00 8.29236 3.92628 4.97243 MACS2_peak_21 +chr1 3341408 3341661 254 3341461 3.00 7.77216 3.90105 4.60940 MACS2_peak_22 +chr1 3369639 3369892 254 3369863 3.00 8.29236 3.92628 4.97243 MACS2_peak_23 +chr1 3400441 3400769 329 3400610 4.00 10.71801 4.90785 7.08620 MACS2_peak_24 +chr1 3407841 3408094 254 3407975 3.00 8.29236 3.92628 4.97243 MACS2_peak_25 +chr1 3481748 3482245 498 3481863 4.00 10.71801 4.90785 7.08620 MACS2_peak_26 +chr1 3535562 3535821 260 3535663 3.00 8.29236 3.92628 4.97243 MACS2_peak_27 +chr1 3537757 3538010 254 3537960 3.00 8.29236 3.92628 4.97243 MACS2_peak_28 +chr1 3593610 3593863 254 3593838 3.00 7.77216 3.90105 4.60940 MACS2_peak_29 +chr1 3640884 3641366 483 3641134 12.00 30.54970 12.67843 24.90331 MACS2_peak_30 +chr1 3702144 3702397 254 3702260 3.00 7.77216 3.90105 4.60940 MACS2_peak_31 +chr1 3773699 3774058 360 3773876 7.00 18.42402 7.85256 13.89198 MACS2_peak_32 +chr1 3827306 3827722 417 3827525 5.00 13.22276 5.88942 9.29290 MACS2_peak_33 +chr1 4712784 4713037 254 4712904 3.00 8.29236 3.92628 4.97243 MACS2_peak_34 +chr1 4886187 4886440 254 4886326 3.00 7.77216 3.90105 4.60940 MACS2_peak_35 +chr1 5569919 5570198 280 5570056 4.00 10.71801 4.90785 7.08620 MACS2_peak_36 +chr1 5574777 5575080 304 5574838 3.00 8.29236 3.92628 4.97243 MACS2_peak_37 +chr1 5805838 5806091 254 5805965 2.00 5.96348 2.94471 2.92914 MACS2_peak_38 +chr1 5976146 5976399 254 5976235 3.00 8.29236 3.92628 4.97243 MACS2_peak_39 +chr1 6094646 6094899 254 6094678 2.00 5.96348 2.94471 2.92914 MACS2_peak_40 +chr1 6112957 6113210 254 6113135 3.00 6.57684 3.80689 3.50364 MACS2_peak_41 +chr1 6265253 6265640 388 6265437 6.00 11.56197 6.50502 7.91704 MACS2_peak_42 +chr1 6305229 6305482 254 6305299 3.00 8.29236 3.92628 4.97243 MACS2_peak_43 +chr1 6306874 6307127 254 6307013 3.00 8.29236 3.92628 4.97243 MACS2_peak_44 +chr1 6403481 6403843 363 6403679 6.00 15.79441 6.87099 11.56042 MACS2_peak_45 +chr1 6464657 6465096 440 6464869 6.00 11.56197 6.50502 7.91704 MACS2_peak_46 +chr1 6483604 6483857 254 6483739 3.00 8.29236 3.92628 4.97243 MACS2_peak_47 +chr1 6498110 6498494 385 6498258 6.00 14.88256 6.82684 10.84922 MACS2_peak_48 +chr1 6535513 6535838 326 6535591 5.00 13.22276 5.88942 9.29290 MACS2_peak_49 +chr1 6614468 6614882 415 6614708 4.00 10.06728 4.87632 6.61759 MACS2_peak_50 +chr1 6706586 6706931 346 6706743 5.00 13.22276 5.88942 9.29290 MACS2_peak_51 +chr1 6761833 6762203 371 6762039 7.00 14.98313 7.61377 10.92185 MACS2_peak_52 +chr1 6780092 6780471 380 6780329 6.00 15.79441 6.87099 11.56042 MACS2_peak_53 +chr1 6787475 6787900 426 6787704 7.00 18.42402 7.85256 13.89198 MACS2_peak_54 +chr1 6949953 6950377 425 6950153 5.00 10.64473 5.71033 7.08620 MACS2_peak_55 +chr1 7102753 7103077 325 7102915 4.00 10.71801 4.90785 7.08620 MACS2_peak_56 +chr1 7278317 7278718 402 7278483 6.00 15.79441 6.87099 11.56042 MACS2_peak_57 +chr1 7868456 7868722 267 7868577 4.00 10.71801 4.90785 7.08620 MACS2_peak_58 +chr1 7962797 7963068 272 7962862 3.00 7.77216 3.90105 4.60940 MACS2_peak_59 +chr1 8042368 8042722 355 8042491 6.00 14.88256 6.82684 10.84922 MACS2_peak_60 +chr1 8075039 8075466 428 8075252 6.00 12.78498 6.66205 9.02328 MACS2_peak_61 +chr1 8076577 8076851 275 8076739 4.00 8.57130 4.75861 5.22097 MACS2_peak_62 +chr1 8091217 8091506 290 8091352 4.00 10.71801 4.90785 7.08620 MACS2_peak_63 +chr1 8374359 8374715 357 8374570 6.00 15.79441 6.87099 11.56042 MACS2_peak_64 +chr1 8408996 8409352 357 8409218 4.00 10.71801 4.90785 7.08620 MACS2_peak_65 +chr1 8731417 8731750 334 8731570 4.00 10.06728 4.87632 6.61759 MACS2_peak_66 +chr1 8786590 8786948 359 8786756 7.00 12.59445 7.26312 8.86075 MACS2_peak_67 +chr1 8908916 8909169 254 8909002 2.00 5.57376 2.92579 2.70690 MACS2_peak_68 +chr1 8978204 8978524 321 8978356 5.00 13.22276 5.88942 9.29290 MACS2_peak_69 +chr1 9048092 9048380 289 9048260 4.00 8.57130 4.75861 5.22097 MACS2_peak_70 +chr1 9065105 9065592 488 9065349 5.00 13.22276 5.88942 9.29290 MACS2_peak_71 +chr1 9069997 9070429 433 9070211 4.00 10.71801 4.90785 7.08620 MACS2_peak_72 |
| b |
| diff -r ce0f144f4835 -r f0ec41881020 test-data/macs_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/macs_2.txt Mon Aug 06 10:42:11 2018 -0400 |
| [ |
| @@ -0,0 +1,100 @@ +# This file is generated by MACS version 2.1.1.20160309 +# Command line: callpeak --name treat2 -t /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpiNVEd5/files/000/dataset_8.dat -c /private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpiNVEd5/files/000/dataset_2.dat --format BED --gsize 2700000000 --keep-dup 1 --qvalue 0.05 --mfold 5 50 --bw 300 +# ARGUMENTS LIST: +# name = treat2 +# format = BED +# ChIP-seq file = ['/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpiNVEd5/files/000/dataset_8.dat'] +# control file = ['/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpiNVEd5/files/000/dataset_2.dat'] +# effective genome size = 2.70e+09 +# band width = 300 +# model fold = [5, 50] +# qvalue cutoff = 5.00e-02 +# Larger dataset will be scaled towards smaller dataset. +# Range for calculating regional lambda is: 1000 bps and 10000 bps +# Broad region calling is off +# Paired-End mode is off + +# tag size is determined as 100 bps +# total tags in treatment: 100000 +# tags after filtering in treatment: 99795 +# maximum duplicate tags at the same position in treatment = 1 +# Redundant rate in treatment: 0.00 +# total tags in control: 199978 +# tags after filtering in control: 199867 +# maximum duplicate tags at the same position in control = 1 +# Redundant rate in control: 0.00 +# d = 254 +# alternative fragment length(s) may be 254 bps +chr start end length abs_summit pileup -log10(pvalue) fold_enrichment -log10(qvalue) name +chr1 115538 115791 254 115665 1.00 4.35859 1.98140 1.67749 MACS2_peak_1 +chr1 237644 237935 292 237790 2.00 6.86347 2.97210 3.86269 MACS2_peak_2 +chr1 542564 542817 254 542691 1.00 4.35859 1.98140 1.67749 MACS2_peak_3 +chr1 652482 652735 254 652609 1.00 4.35859 1.98140 1.67749 MACS2_peak_4 +chr1 675967 676220 254 676094 1.00 4.35859 1.98140 1.67749 MACS2_peak_5 +chr1 739125 739378 254 739252 1.00 4.35859 1.98140 1.67749 MACS2_peak_6 +chr1 785730 785983 254 785857 1.00 4.35859 1.98140 1.67749 MACS2_peak_7 +chr1 805192 805536 345 805364 2.00 6.47268 2.96243 3.63723 MACS2_peak_8 +chr1 811789 812361 573 811916 1.00 3.49990 1.95053 1.44931 MACS2_peak_9 +chr1 840079 840401 323 840240 4.00 12.21969 4.95350 8.64187 MACS2_peak_10 +chr1 858769 859114 346 858942 2.00 6.47268 2.96243 3.63723 MACS2_peak_11 +chr1 875785 876038 254 875912 1.00 4.09830 1.97495 1.67749 MACS2_peak_12 +chr1 902086 902339 254 902213 1.00 4.09830 1.97495 1.67749 MACS2_peak_13 +chr1 911342 911595 254 911469 1.00 4.35859 1.98140 1.67749 MACS2_peak_14 +chr1 919315 919929 615 919550 5.00 14.24284 5.92486 10.53337 MACS2_peak_15 +chr1 937147 937603 457 937375 4.00 11.56776 4.93738 8.14431 MACS2_peak_16 +chr1 953008 953261 254 953135 1.00 4.35859 1.98140 1.67749 MACS2_peak_17 +chr1 954263 955017 755 954814 3.00 9.49316 3.96280 6.20710 MACS2_peak_18 +chr1 994723 995089 367 994906 3.00 9.49316 3.96280 6.20710 MACS2_peak_19 +chr1 999268 999578 311 999423 2.00 6.86347 2.97210 3.86269 MACS2_peak_20 +chr1 1004656 1004909 254 1004783 1.00 4.35859 1.98140 1.67749 MACS2_peak_21 +chr1 1044551 1044804 254 1044678 1.00 4.35859 1.98140 1.67749 MACS2_peak_22 +chr1 1057326 1057692 367 1057509 3.00 9.49316 3.96280 6.20710 MACS2_peak_23 +chr1 1105615 1105868 254 1105742 1.00 3.49990 1.95053 1.44931 MACS2_peak_24 +chr1 1115032 1115285 254 1115159 1.00 4.35859 1.98140 1.67749 MACS2_peak_25 +chr1 1142348 1142601 254 1142475 1.00 4.09830 1.97495 1.67749 MACS2_peak_26 +chr1 1143298 1143551 254 1143425 1.00 4.09830 1.97495 1.67749 MACS2_peak_27 +chr1 1166225 1166478 254 1166352 1.00 4.35859 1.98140 1.67749 MACS2_peak_28 +chr1 1204174 1204427 254 1204301 1.00 4.35859 1.98140 1.67749 MACS2_peak_29 +chr1 1220904 1221157 254 1221031 1.00 4.09830 1.97495 1.67749 MACS2_peak_30 +chr1 1225704 1225957 254 1225831 1.00 4.35859 1.98140 1.67749 MACS2_peak_31 +chr1 1227178 1227443 266 1227311 2.00 6.86347 2.97210 3.86269 MACS2_peak_32 +chr1 1240549 1241123 575 1240777 3.00 8.97181 3.94991 5.83616 MACS2_peak_33 +chr1 1241426 1241846 421 1241636 2.00 6.47268 2.96243 3.63723 MACS2_peak_34 +chr1 1284325 1284888 564 1284452 1.00 4.35859 1.98140 1.67749 MACS2_peak_35 +chr1 1307376 1307825 450 1307601 5.00 14.24284 5.92486 10.53337 MACS2_peak_36 +chr1 1310554 1310807 254 1310681 1.00 4.09830 1.97495 1.67749 MACS2_peak_37 +chr1 1316444 1316697 254 1316571 1.00 4.09830 1.97495 1.67749 MACS2_peak_38 +chr1 1318227 1318480 254 1318354 1.00 4.35859 1.98140 1.67749 MACS2_peak_39 +chr1 1334774 1335027 254 1334901 1.00 3.49990 1.95053 1.44931 MACS2_peak_40 +chr1 1365743 1365996 254 1365870 1.00 4.09830 1.97495 1.67749 MACS2_peak_41 +chr1 1406356 1406609 254 1406483 1.00 4.35859 1.98140 1.67749 MACS2_peak_42 +chr1 1440209 1440715 507 1440462 4.00 12.21969 4.95350 8.64187 MACS2_peak_43 +chr1 1440989 1441242 254 1441116 1.00 4.35859 1.98140 1.67749 MACS2_peak_44 +chr1 1487432 1487685 254 1487559 1.00 4.09830 1.97495 1.67749 MACS2_peak_45 +chr1 1506072 1506325 254 1506199 1.00 4.09830 1.97495 1.67749 MACS2_peak_46 +chr1 1549214 1549467 254 1549341 1.00 4.09830 1.97495 1.67749 MACS2_peak_47 +chr1 1555404 1555738 335 1555571 4.00 12.21969 4.95350 8.64187 MACS2_peak_48 +chr1 1556892 1557145 254 1557019 1.00 4.35859 1.98140 1.67749 MACS2_peak_49 +chr1 1590595 1591084 490 1590840 4.00 11.56776 4.93738 8.14431 MACS2_peak_50 +chr1 1609355 1609608 254 1609482 1.00 4.35859 1.98140 1.67749 MACS2_peak_51 +chr1 1610353 1610772 420 1610563 2.00 6.86347 2.97210 3.86269 MACS2_peak_52 +chr1 1619961 1620214 254 1620088 1.00 4.09830 1.97495 1.67749 MACS2_peak_53 +chr1 1655695 1656225 531 1655822 1.00 4.09830 1.97495 1.67749 MACS2_peak_54 +chr1 1657692 1657945 254 1657819 1.00 4.09830 1.97495 1.67749 MACS2_peak_55 +chr1 1680363 1680616 254 1680490 1.00 4.35859 1.98140 1.67749 MACS2_peak_56 +chr1 1720444 1720697 254 1720571 1.00 4.35859 1.98140 1.67749 MACS2_peak_57 +chr1 1728043 1728296 254 1728170 1.00 4.09830 1.97495 1.67749 MACS2_peak_58 +chr1 1734745 1734998 254 1734872 1.00 4.35859 1.98140 1.67749 MACS2_peak_59 +chr1 1743661 1743914 254 1743788 1.00 4.09830 1.97495 1.67749 MACS2_peak_60 +chr1 1756326 1756579 254 1756453 1.00 3.49990 1.95053 1.44931 MACS2_peak_61 +chr1 1760856 1761109 254 1760983 1.00 3.49990 1.95053 1.44931 MACS2_peak_62 +chr1 1766488 1766741 254 1766615 1.00 3.49990 1.95053 1.44931 MACS2_peak_63 +chr1 1787177 1787430 254 1787304 1.00 4.35859 1.98140 1.67749 MACS2_peak_64 +chr1 1791336 1791589 254 1791463 1.00 4.09830 1.97495 1.67749 MACS2_peak_65 +chr1 1830665 1830918 254 1830792 1.00 4.09830 1.97495 1.67749 MACS2_peak_66 +chr1 1837638 1838133 496 1837886 6.00 16.98484 6.91233 12.98445 MACS2_peak_67 +chr1 1839919 1840172 254 1840046 1.00 4.09830 1.97495 1.67749 MACS2_peak_68 +chr1 1840298 1841007 710 1840547 5.00 15.02536 5.94420 11.12772 MACS2_peak_69 +chr1 1891434 1891687 254 1891561 1.00 4.35859 1.98140 1.67749 MACS2_peak_70 +chr1 1938174 1938427 254 1938301 1.00 4.35859 1.98140 1.67749 MACS2_peak_71 +chr1 1974716 1975076 361 1974896 2.00 6.47268 2.96243 3.63723 MACS2_peak_72 |
| b |
| diff -r ce0f144f4835 -r f0ec41881020 test-data/macs_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/macs_stats.tabular Mon Aug 06 10:42:11 2018 -0400 |
| b |
| @@ -0,0 +1,3 @@ +Sample fragment_size treatment_fragments_total treatment_fragments_after_filtering treatment_max_duplicates treatment_redundant_rate control_fragments_total control_fragments_after_filtering control_max_duplicates control_redundant_rate d +treat1 100.0 199977.0 199583.0 1.0 0.0 199978.0 199867.0 1.0 0.0 254.0 +treat2 100.0 100000.0 99795.0 1.0 0.0 199978.0 199867.0 1.0 0.0 254.0 |