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multiqc/.shed.yml multiqc/multiqc.xml multiqc/readme.rst multiqc/test-data/CollectInsertSizeMetrics.txt multiqc/test-data/MarkDuplicates_data.txt multiqc/test-data/bismark_data.txt multiqc/test-data/bowtie2SE1.txt multiqc/test-data/bowtie2SE2.txt multiqc/test-data/collectGcBias_data.txt multiqc/test-data/cutadapt.txt multiqc/test-data/fastqc_data.txt multiqc/test-data/fastqc_data_2.txt multiqc/test-data/featurecounts_data.txt multiqc/test-data/htseq_data.txt multiqc/test-data/log_fastqc.txt multiqc/test-data/picard_CollectAlignmentSummaryMetrics.txt multiqc/test-data/picard_CollectBaseDistributionByCycle.txt multiqc/test-data/picard_CollectRnaSeqMetrics.txt multiqc/test-data/report_all.html multiqc/test-data/report_bismark.html multiqc/test-data/report_bowtie2SE.html multiqc/test-data/report_cutadapt.html multiqc/test-data/report_fastqc.html multiqc/test-data/report_fastqc_2.html multiqc/test-data/report_featurecounts.html multiqc/test-data/report_htseq.html multiqc/test-data/report_picard.html multiqc/test-data/report_rnastar_counts.html multiqc/test-data/report_rnastar_log.html multiqc/test-data/report_samtools.html multiqc/test-data/report_samtools_idxstats.html multiqc/test-data/report_tophat.html multiqc/test-data/rnastar_counts.txt multiqc/test-data/rnastar_log.txt multiqc/test-data/samtools_flagstat.txt multiqc/test-data/samtools_idxstats.txt multiqc/test-data/samtools_stats.txt multiqc/test-data/tophat_data.txt |
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multiqc.xml readme.rst test-data/CollectInsertSizeMetrics.txt test-data/MarkDuplicates_data.txt test-data/bismark_data.txt test-data/collectGcBias_data.txt test-data/cutadapt.txt test-data/fastqc_data.txt test-data/fastqc_data_2.txt test-data/featurecounts_data.txt test-data/log_all.txt test-data/log_bismark.txt test-data/log_cutadapt.txt test-data/log_fastqc.txt test-data/log_fastqc_2.txt test-data/log_featurecounts.txt test-data/log_picard.txt test-data/log_samtools.txt test-data/log_tophat.txt test-data/report_all.html test-data/report_bismark.html test-data/report_cutadapt.html test-data/report_fastqc.html test-data/report_fastqc_2.html test-data/report_featurecounts.html test-data/report_picard.html test-data/report_samtools.html test-data/report_tophat.html test-data/samtools_data.txt test-data/tophat_data.txt tool_dependencies.xml |
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| diff -r 66f1187ed363 -r 4612d775965f multiqc.xml --- a/multiqc.xml Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,241 +0,0 @@\n-<tool id="multiqc" name="multiqc" version="0.6">\n- <description>aggregate results from bioinformatics analyses across many samples into a single report</description>\n- <requirements>\n- <requirement type="package" version="0.6">multiqc</requirement>\n- <requirement type="package" version="1.6.7">libpng</requirement>\n- </requirements>\n- <stdio>\n- <exit_code range="1:" />\n- </stdio>\n- <command>\n- mkdir multiqc_WDir;\n- \n- #for $i, $repeat in enumerate( $results )\n-\n- mkdir multiqc_WDir/${repeat.software}_${i};\n-\n- #if str($repeat.software) == "fastqc"\n-\n- #for $k, $file in enumerate ( $repeat.input_file )\n- ## create a directory for each file because of the unqiue name file parsing\n- mkdir multiqc_WDir/${repeat.software}_${i}/file_${k};\n- ##cat ${file} > multiqc_WDir/${repeat.software}_${i}/file_$k/fastqc_data.txt;\n- ln -s ${file} multiqc_WDir/${repeat.software}_${i}/file_$k/fastqc_data.txt;\n- #end for \n-\n- #else if str($repeat.software) == "tophat"\n-\n- #for $file in $repeat.input_file\n- ## test if input file name contains align_summary\n- if [[ \'${file.display_name}\' =~ align_summary$ ]]; then\n- ##cat ${file} > multiqc_WDir/${repeat.software}_${i}/\'${file.display_name}\'.txt; else\n- ln -s ${file} multiqc_WDir/${repeat.software}_${i}/\'${file.display_name}\'.txt; else\n- ##cat ${file} > multiqc_WDir/${repeat.software}_${i}/\'${file.display_name}\'_align_summary.txt; \n- ln -s ${file} multiqc_WDir/${repeat.software}_${i}/\'${file.display_name}\'_align_summary.txt;\n- fi;\n- #end for\n-\n- #else if str($repeat.software) == "cutadapt"\n-\n- #for $file in $repeat.input_file\n- cat ${file} > multiqc_WDir/${repeat.software}_${i}/\'${file.display_name}\'.txt;\n- ## replace header for old cutadapt release\n- sed -i \'s/You are running/This is/\' multiqc_WDir/${repeat.software}_${i}/\'${file.display_name}\'.txt; \n- #end for\n-\n- #else if str($repeat.software) == "featurecounts"\n-\n- #for $file in $repeat.input_file\n- ## remove spaces and colon to skip multiqc crash\n- cat ${file} > multiqc_WDir/${repeat.software}_${i}/featurecounts_result.summary;\n- ## remove spaces and colon to skip multiqc crash\n- sed -i \'s/:/_/g\' multiqc_WDir/${repeat.software}_${i}/featurecounts_result.summary;\n- sed -i \'s/ /_/g\' multiqc_WDir/${repeat.software}_${i}/featurecounts_result.summary;\n- #end for\n-\n- #else if str($repeat.software) == "bismark"\n-\n- #for $file in $repeat.input_file\n- ##cat ${file} > multiqc_WDir/${repeat.software}_${i}/\'${file.display_name}\'_SE_report.txt;\n- ln -s ${file} multiqc_WDir/${repeat.software}_${i}/\'${file.display_name}\'_SE_report.txt;\n- #end for\n-\n- #else\n-\n- #for $file in $repeat.input_file\n- cat ${file} > multiqc_WDir/${repeat.software}_${i}/\'${file.display_name}\';\n- #if str($repeat.software) == "picard"\n-\t\t sed -i \'s/picard.sam.markduplicates.MarkDuplicates/picard.sam.MarkDuplicates/\' multiqc_WDir/${repeat.software}_${i}/\'${file.display_name}\'; \n-\t\t #end if\n- #end for \n-\n- #end if\n- #end for\n-\n- multiqc multiqc_WDir; \n- \n- </command>\n- <inputs>\n- <!--param name="inputs" type="data" format="txt" multiple="true" label="Tools logs-outputs" /-->\n- <repeat name="results" title="Results" min="1">\n- <param name="software" type="select" label="Software name">\n- '..b'ecounts_data.txt" />\n- </repeat>\n- <output name="html_file" file="report_featurecounts.html" compare="sim_size" delta="1000"/>\n- <output name="text_file" file="log_featurecounts.txt" compare="sim_size" delta="1000"/>\n- </test>\n- <test>\n- <repeat name="results">\n- <param name="software" value="picard" />\n- <param name="input_file" value="collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt" />\n- </repeat>\n- <output name="html_file" file="report_picard.html" compare="sim_size" delta="1000"/>\n- <output name="text_file" file="log_picard.txt" compare="sim_size" delta="1000"/>\n- </test>\n- <test>\n- <repeat name="results">\n- <param name="software" value="bismark" />\n- <param name="input_file" value="bismark_data.txt" />\n- </repeat>\n- <output name="html_file" file="report_bismark.html" compare="sim_size" delta="1000"/>\n- <output name="text_file" file="log_bismark.txt" compare="sim_size" delta="1000"/>\n- </test>\n- <test>\n- <repeat name="results">\n- <param name="software" value="samtools_stats" />\n- <param name="input_file" value="samtools_data.txt" />\n- </repeat>\n- <output name="html_file" file="report_samtools.html" compare="sim_size" delta="1000"/>\n- <output name="text_file" file="log_samtools.txt" compare="sim_size" delta="1000"/>\n- </test>\n- <test>\n- <repeat name="results">\n- <param name="software" value="fastqc" />\n- <param name="input_file" value="fastqc_data.txt,fastqc_data_2.txt" />\n- </repeat>\n- <repeat name="results">\n- <param name="software" value="cutadapt" />\n- <param name="input_file" value="cutadapt.txt" />\n- </repeat>\n- <repeat name="results">\n- <param name="software" value="tophat" />\n- <param name="input_file" value="tophat_data.txt" />\n- </repeat>\n- <repeat name="results">\n- <param name="software" value="featurecounts" />\n- <param name="input_file" value="featurecounts_data.txt" />\n- </repeat>\n- <repeat name="results">\n- <param name="software" value="picard" />\n- <param name="input_file" value="collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt" />\n- </repeat>\n- <repeat name="results">\n- <param name="software" value="bismark" />\n- <param name="input_file" value="bismark_data.txt" />\n- </repeat>\n- <repeat name="results">\n- <param name="software" value="samtools_stats" />\n- <param name="input_file" value="samtools_data.txt" />\n- </repeat>\n-\n- <output name="html_file" file="report_all.html" compare="sim_size" delta="3000"/>\n- <output name="text_file" file="log_all.txt" compare="sim_size" delta="3000"/>\n- </test>\n- </tests>\n-\n-\n- <help>\n-**What it does**\n-\n-MultiQC aggregates results from bioinformatics analyses across many samples into a single report\n-\n-----\n-\n-**Description**\n-\n-MultiQC searches a given directory for analysis logs and compiles a HTML report. It\'s a general use tool, perfect for summarising the output from numerous bioinformatics tools.\n-\n-----\n-\n-**Inputs**\n-\n-MultiQC takes software outputs summary in order to create a single report. Below a list of compatible Galaxy tools :\n-\n- - Fastqc\n- - Cutadapt\n- - Tophat2\n- - FeatureCounts\n- - Samtools stats\n- - Picard MarkDuplicates metrics\n- - Picard CollectGTBiasMetrics\n- - Picard CollectInsertSizeMetrics\n- - Bismark\n-\n-----\n-\n-**Integrated by:**\n-\n-Cyril Monjeaud and Yvan Le Bras\n-\n-`EnginesOn <http://engineson.fr/>`_ and Rennes GenOuest Bio-informatics Core Facility\n-\n- </help>\n-\n- <citations>\n- <citation type="doi">10.1093/bioinformatics/btw354</citation>\n- </citations>\n-</tool>\n-\n' |
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| diff -r 66f1187ed363 -r 4612d775965f multiqc/.shed.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/.shed.yml Thu May 25 17:49:13 2017 -0400 |
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| @@ -0,0 +1,12 @@ +categories: +- Fastq Manipulation +- Statistics +description: multiqc tool +name: multiqc +owner: engineson +long_description: | + MultiQC searches a given directory for analysis logs and compiles a HTML report. + It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. +homepage_url: http://multiqc.info/ +remote_repository_url: https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc +type: unrestricted |
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| diff -r 66f1187ed363 -r 4612d775965f multiqc/multiqc.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/multiqc.xml Thu May 25 17:49:13 2017 -0400 |
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| b'@@ -0,0 +1,271 @@\n+<tool id="multiqc" name="multiqc" version="1.0.0.0">\n+ <description>aggregate results from bioinformatics analyses into a single report</description>\n+ <requirements>\n+ <requirement type="package" version="1.0.0">multiqc</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" />\n+ </stdio>\n+ <command>\n+ mkdir multiqc_WDir;\n+ \n+ #for $i, $repeat in enumerate( $results )\n+ mkdir multiqc_WDir/${repeat.software}_${i};\n+\n+ #if str($repeat.software) == "fastqc":\n+ ## Searches for files named "fastqc_data.txt"\n+ #for $k, $file in enumerate($repeat.input_file):\n+ mkdir multiqc_WDir/${repeat.software}_${i}/file_${k};\n+ ln -s \'${file}\' multiqc_WDir/fastqc_${i}/file_${k}/fastqc_data.txt;\n+ #end for \n+ #else if str($repeat.software) == "tophat":\n+ ## Searches for files ending in "align_summary.txt"\n+ #for $file in $repeat.input_file:\n+ ln -s \'${file}\' \'multiqc_WDir/${repeat.software}_${i}/${file.display_name}align_summary.txt\';\n+ #end for\n+ #else if str($repeat.software) == "bowtie2":\n+ ## Searches for files containing \'reads; of these;\'\n+ #for $file in $repeat.input_file:\n+ ln -s \'${file}\' \'multiqc_WDir/${repeat.software}_${i}/${file.display_name}.txt\';\n+ #end for\n+ #else if str($repeat.software) == "cutadapt":\n+ ## Searches for files containing \'This is cutadapt\'\n+ #for $file in $repeat.input_file:\n+ cat \'${file}\' > \'multiqc_WDir/${repeat.software}_${i}/${file.display_name}.txt\';\n+ ## replace header for old cutadapt release\n+ sed -i .old \'s/You are running/This is/\' \'multiqc_WDir/${repeat.software}_${i}/${file.display_name}.txt\'; \n+ #end for\n+ #else if str($repeat.software) == "featurecounts":\n+ ## Checks for files ending in \'.summary\'\n+ #for $k, $file in enumerate($repeat.input_file):\n+ mkdir multiqc_WDir/${repeat.software}_${i}/file_${k};\n+ ln -s \'${file}\' \'multiqc_WDir/${repeat.software}_${i}/file_${k}/${file.display_name}.summary\';\n+ #end for\n+ #else if str($repeat.software) == "bismark":\n+ ## Checks for files ending in _SE_report.txt\n+ #for $file in $repeat.input_file\n+ ln -s ${file} \'multiqc_WDir/${repeat.software}_${i}/${file.display_name}_SE_report.txt\';\n+ #end for\n+ #else if str($repeat.software) == "samtools":\n+ ## Checks for files containing \'This file was produced by samtools stats\'\n+ #for $file in $repeat.input_file\n+ ln -s ${file} \'multiqc_WDir/${repeat.software}_${i}/${file.display_name}\';\n+ #end for\n+ #else if str($repeat.software) == "picard":\n+ #for $file in $repeat.input_file\n+ ln -s \'${file}\' \'multiqc_WDir/${repeat.software}_${i}/${file.display_name}\';\n+ #end for \n+ #else if str($repeat.software) == "samtools_idxstats":\n+ ## Checks for files containing "idxstats" in the name\n+ #for $file in $repeat.input_file\n+ ln -s \'${file}\' \'multiqc_WDir/${repeat.software}_${i}/${file.display_name}_idxstats.txt\';\n+ #end for \n+ #else if str($repeat.software) == "htseq":\n+ ## Checks for files containing "__too_low_aQual"\n+ #for $file in $repeat.input_file\n+ ln -s \'${file}\' \'multiqc_WDir/${repeat.software}_${i}/${file.display_name}\';\n+ #end for \n+ #else if str($repeat.software) == "rnastar_log":\n+ '..b'test>\n+ <test>\n+ <repeat name="results">\n+ <param name="software" value="bismark" />\n+ <param name="input_file" value="bismark_data.txt" />\n+ </repeat>\n+ <output name="html_file" file="report_bismark.html" compare="sim_size" delta="1000"/>\n+ </test>\n+ <test>\n+ <repeat name="results">\n+ <param name="software" value="samtools" />\n+ <param name="input_file" value="samtools_stats.txt,samtools_flagstat.txt" />\n+ </repeat>\n+ <output name="html_file" file="report_samtools.html" compare="sim_size" delta="1000"/>\n+ </test>\n+ <test>\n+ <repeat name="results">\n+ <param name="software" value="samtools_idxstats" />\n+ <param name="input_file" value="samtools_idxstats.txt" />\n+ </repeat>\n+ <output name="html_file" file="report_samtools_idxstats.html" compare="sim_size" delta="1000"/>\n+ </test>\n+ <test>\n+ <repeat name="results">\n+ <param name="software" value="fastqc" />\n+ <param name="input_file" value="fastqc_data.txt,fastqc_data_2.txt" />\n+ </repeat>\n+ <repeat name="results">\n+ <param name="software" value="cutadapt" />\n+ <param name="input_file" value="cutadapt.txt" />\n+ </repeat>\n+ <repeat name="results">\n+ <param name="software" value="tophat" />\n+ <param name="input_file" value="tophat_data.txt" />\n+ </repeat>\n+ <repeat name="results">\n+ <param name="software" value="featurecounts" />\n+ <param name="input_file" value="featurecounts_data.txt" />\n+ </repeat>\n+ <repeat name="results">\n+ <param name="software" value="picard" />\n+ <param name="input_file" value="collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt" />\n+ </repeat>\n+ <repeat name="results">\n+ <param name="software" value="bismark" />\n+ <param name="input_file" value="bismark_data.txt" />\n+ </repeat>\n+ <repeat name="results">\n+ <param name="software" value="samtools" />\n+ <param name="input_file" value="samtools_stats.txt,samtools_flagstat.txt" />\n+ </repeat>\n+ <output name="html_file" file="report_all.html" compare="sim_size" delta="5000"/>\n+ </test>\n+ </tests>\n+\n+ <help>\n+**What it does**\n+\n+MultiQC aggregates results from bioinformatics analyses across many samples into a single report. It takes results of multiple analyses and creates a report that can be viewed as a single beautiful web-page. It\'s a general use tool, perfect for summarizing the output from numerous bioinformatics tools.\n+\n+**Inputs**\n+\n+MultiQC takes software output summaries/logs and creates a single report from them. You need to tell the tool which software was used to generate the report. This is done using the **Software name** dropdown. At present the following Galaxy tools produce logs that can used with MultiQC. There are:\n+\n+- Fastqc\n+- Cutadapt / Trim Galore!\n+- Tophat2\n+- FeatureCounts\n+- Samtools (stats, flagstat, dxstats)\n+- Picard (MarkDuplicatesMetrics, CollectGCBiasMetrics, CollectInsertSizeMetrics, CollectAlignmentSummaryMetrics, CollectRnaSeqMetrics)\n+- Bismark (Alignment report file)\n+- Bowtie2 (Metrics file)\n+- HTSeq-count ("no feature" file; although the "Assigned" metric is always 0)\n+- RNA STAR (Alignment from Log.final.out, Gene counts from ReadsPerGene.out.tab)\n+\n+----\n+\n+**Integrated by**\n+\n+Cyril Monjeaud and Yvan Le Bras\n+\n+`EnginesOn <http://engineson.fr/>`_ and Rennes GenOuest Bio-informatics Core Facility\n+\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btw354</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 66f1187ed363 -r 4612d775965f multiqc/readme.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/readme.rst Thu May 25 17:49:13 2017 -0400 |
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| @@ -0,0 +1,36 @@ +======================== +Galaxy multiqc wrapper +======================== + +Aggregate results from bioinformatics analyses across many samples into a single report + +MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. + +============ +Installation +============ + +Requirements: pkg-config + +Conda recipe: A conda recipe exists in bioconda repository. If you have a recent Galaxy release, the packages installation is not mandatory. + +================ +MultiQC webpage +================ + +Important: For a good view of multiqc webpage, you need to deactivate the sanitize_all_html option in galaxy.ini + + sanitize_all_html = False + +======= +History +======= + + * v1.0.0.0 Update to multiQC 1.0, add additional supported tools + * v0.6: Initial public release + +========== +Citation +========== + +Created by EnginesOn company |
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| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/CollectInsertSizeMetrics.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/CollectInsertSizeMetrics.txt Thu May 25 17:49:13 2017 -0400 |
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| @@ -0,0 +1,737 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=/omaha-beach/cloud_26/files/000/dataset_199.dat DEVIATIONS=10.0 MINIMUM_PCT=0.05 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=/omaha-beach/cloud_26/files/000/dataset_197.dat OUTPUT=/omaha-beach/cloud_26/files/000/dataset_198.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json +## htsjdk.samtools.metrics.StringHeader +# Started on: Mon May 23 09:33:00 UTC 2016 + +## METRICS CLASS picard.analysis.InsertSizeMetrics +MEDIAN_INSERT_SIZE MEDIAN_ABSOLUTE_DEVIATION MIN_INSERT_SIZE MAX_INSERT_SIZE MEAN_INSERT_SIZE STANDARD_DEVIATION READ_PAIRS PAIR_ORIENTATION WIDTH_OF_10_PERCENT WIDTH_OF_20_PERCENT WIDTH_OF_30_PERCENT WIDTH_OF_40_PERCENT WIDTH_OF_50_PERCENT WIDTH_OF_60_PERCENT WIDTH_OF_70_PERCENT WIDTH_OF_80_PERCENT WIDTH_OF_90_PERCENT WIDTH_OF_99_PERCENT SAMPLE LIBRARY READ_GROUP +194 63 100 5331452 271.809759 196.076488 311788 FR 25 47 69 91 127 343 941 1515 2585 16663 + +## HISTOGRAM java.lang.Integer +insert_size All_Reads.fr_count +100 2 +101 117 +102 424 +103 390 +104 376 +105 335 +106 360 +107 343 +108 353 +109 386 +110 349 +111 368 +112 445 +113 459 +114 470 +115 512 +116 478 +117 520 +118 558 +119 599 +120 603 +121 600 +122 696 +123 703 +124 657 +125 747 +126 734 +127 753 +128 820 +129 880 +130 923 +131 931 +132 953 +133 1006 +134 1086 +135 1134 +136 1177 +137 1280 +138 1381 +139 1419 +140 1494 +141 1625 +142 1697 +143 1838 +144 1899 +145 1957 +146 2197 +147 2214 +148 2276 +149 2450 +150 2557 +151 2523 +152 2619 +153 2591 +154 2575 +155 2745 +156 2756 +157 2716 +158 2765 +159 2775 +160 2884 +161 2830 +162 2781 +163 2718 +164 2777 +165 2859 +166 2803 +167 2855 +168 2896 +169 2817 +170 2843 +171 2817 +172 2844 +173 2855 +174 2777 +175 2684 +176 2703 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| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/MarkDuplicates_data.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/MarkDuplicates_data.txt Thu May 25 17:49:13 2017 -0400 |
| [ |
| @@ -0,0 +1,112 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.sam.markduplicates.MarkDuplicates INPUT=[/omaha-beach/cloud_26/files/000/dataset_114.dat] OUTPUT=/omaha-beach/cloud_26/files/000/dataset_197.dat METRICS_FILE=/omaha-beach/cloud_26/files/000/dataset_196.dat REMOVE_DUPLICATES=false ASSUME_SORTED=true DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json +## htsjdk.samtools.metrics.StringHeader +# Started on: Mon May 23 09:32:41 UTC 2016 + +## METRICS CLASS picard.sam.DuplicationMetrics +LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE +Unknown Library 2900 313405 0 2257 629 0 0.005582 77973949 + +## HISTOGRAM java.lang.Double +BIN VALUE +1.0 1 +2.0 1.995989 +3.0 2.987982 +4.0 3.975997 +5.0 4.960048 +6.0 5.940152 +7.0 6.916324 +8.0 7.88858 +9.0 8.856937 +10.0 9.821409 +11.0 10.782013 +12.0 11.738763 +13.0 12.691676 +14.0 13.640766 +15.0 14.586049 +16.0 15.52754 +17.0 16.465254 +18.0 17.399207 +19.0 18.329414 +20.0 19.25589 +21.0 20.178649 +22.0 21.097706 +23.0 22.013077 +24.0 22.924776 +25.0 23.832819 +26.0 24.737218 +27.0 25.63799 +28.0 26.535149 +29.0 27.428709 +30.0 28.318684 +31.0 29.20509 +32.0 30.08794 +33.0 30.967248 +34.0 31.84303 +35.0 32.715298 +36.0 33.584068 +37.0 34.449352 +38.0 35.311166 +39.0 36.169523 +40.0 37.024436 +41.0 37.875921 +42.0 38.723989 +43.0 39.568656 +44.0 40.409935 +45.0 41.247839 +46.0 42.082382 +47.0 42.913578 +48.0 43.741439 +49.0 44.565979 +50.0 45.387212 +51.0 46.205151 +52.0 47.019809 +53.0 47.831199 +54.0 48.639334 +55.0 49.444228 +56.0 50.245893 +57.0 51.044342 +58.0 51.839588 +59.0 52.631645 +60.0 53.420524 +61.0 54.206239 +62.0 54.988802 +63.0 55.768226 +64.0 56.544524 +65.0 57.317707 +66.0 58.087789 +67.0 58.854783 +68.0 59.618699 +69.0 60.379551 +70.0 61.137352 +71.0 61.892112 +72.0 62.643845 +73.0 63.392562 +74.0 64.138276 +75.0 64.880999 +76.0 65.620743 +77.0 66.357519 +78.0 67.09134 +79.0 67.822217 +80.0 68.550163 +81.0 69.275188 +82.0 69.997306 +83.0 70.716526 +84.0 71.432862 +85.0 72.146324 +86.0 72.856924 +87.0 73.564674 +88.0 74.269585 +89.0 74.971668 +90.0 75.670935 +91.0 76.367397 +92.0 77.061066 +93.0 77.751952 +94.0 78.440066 +95.0 79.12542 +96.0 79.808025 +97.0 80.487892 +98.0 81.165032 +99.0 81.839456 +100.0 82.511174 + |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/bismark_data.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/bismark_data.txt Thu May 25 17:49:13 2017 -0400 |
| b |
| @@ -0,0 +1,39 @@ +Bismark report for: /omaha-beach/cloud_26/files/000/dataset_33.dat (version: v0.10.0) +Option '--directional' specified: alignments to complementary strands will be ignored (i.e. not performed!) +Bowtie was run against the bisulfite genome of /root/galaxy/database/tmp/tmpvNBPSF/ with the specified options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet + +Final Alignment report +====================== +Sequences analysed in total: 316390 +Number of alignments with a unique best hit from the different alignments: 220558 +Mapping efficiency: 69.7% +Sequences with no alignments under any condition: 93928 +Sequences did not map uniquely: 1904 +Sequences which were discarded because genomic sequence could not be extracted: 0 + +Number of sequences with unique best (first) alignment came from the bowtie output: +CT/CT: 108352 ((converted) top strand) +CT/GA: 112206 ((converted) bottom strand) +GA/CT: 0 (complementary to (converted) top strand) +GA/GA: 0 (complementary to (converted) bottom strand) + +Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 + +Final Cytosine Methylation Report +================================= +Total number of C's analysed: 5291918 + +Total methylated C's in CpG context: 465068 +Total methylated C's in CHG context: 1358074 +Total methylated C's in CHH context: 3449120 +Total methylated C's in Unknown context: 1499 + +Total unmethylated C's in CpG context: 6399 +Total unmethylated C's in CHG context: 2988 +Total unmethylated C's in CHH context: 10269 +Total unmethylated C's in Unknown context: 454 + +C methylated in CpG context: 98.6% +C methylated in CHG context: 99.8% +C methylated in CHH context: 99.7% +C methylated in Unknown context (CN or CHN): 76.8% |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/bowtie2SE1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/bowtie2SE1.txt Thu May 25 17:49:13 2017 -0400 |
| b |
| @@ -0,0 +1,6 @@ +21040602 reads; of these: + 21040602 (100.00%) were unpaired; of these: + 351563 (1.67%) aligned 0 times + 13299463 (63.21%) aligned exactly 1 time + 7389576 (35.12%) aligned >1 times +98.33% overall alignment rate |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/bowtie2SE2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/bowtie2SE2.txt Thu May 25 17:49:13 2017 -0400 |
| b |
| @@ -0,0 +1,6 @@ +16199126 reads; of these: + 16199126 (100.00%) were unpaired; of these: + 274008 (1.69%) aligned 0 times + 10087714 (62.27%) aligned exactly 1 time + 5837404 (36.04%) aligned >1 times +98.31% overall alignment rate |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/collectGcBias_data.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/collectGcBias_data.txt Thu May 25 17:49:13 2017 -0400 |
| [ |
| @@ -0,0 +1,110 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.analysis.CollectGcBiasMetrics CHART_OUTPUT=/omaha-beach/cloud_26/files/000/dataset_195.dat SUMMARY_OUTPUT=/omaha-beach/cloud_26/files/000/dataset_193.dat WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=5.0E-5 IS_BISULFITE_SEQUENCED=true INPUT=/omaha-beach/cloud_26/files/000/dataset_114.dat OUTPUT=/omaha-beach/cloud_26/files/000/dataset_194.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa METRIC_ACCUMULATION_LEVEL=[ALL_READS] STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json +## htsjdk.samtools.metrics.StringHeader +# Started on: Mon May 23 09:32:30 UTC 2016 + +## METRICS CLASS picard.analysis.GcBiasDetailMetrics +ACCUMULATION_LEVEL GC WINDOWS READ_STARTS MEAN_BASE_QUALITY NORMALIZED_COVERAGE ERROR_BAR_WIDTH SAMPLE LIBRARY READ_GROUP +All Reads 0 0 0 0 0 0 +All Reads 1 0 0 0 0 0 +All Reads 2 0 0 0 0 0 +All Reads 3 10 0 0 0 0 +All Reads 4 7 0 0 0 0 +All Reads 5 6 0 0 0 0 +All Reads 6 4 0 0 0 0 +All Reads 7 9 0 0 0 0 +All Reads 8 22 0 0 0 0 +All Reads 9 15 0 0 0 0 +All Reads 10 20 0 0 0 0 +All Reads 11 18 0 0 0 0 +All Reads 12 101 0 0 0 0 +All Reads 13 118 0 0 0 0 +All Reads 14 137 1 20 0.110575 0.110575 +All Reads 15 243 4 19 0.249362 0.124681 +All Reads 16 366 10 21 0.4139 0.130887 +All Reads 17 468 9 24 0.291322 0.097107 +All Reads 18 689 25 24 0.549664 0.109933 +All Reads 19 1087 40 26 0.557451 0.088141 +All Reads 20 2152 95 25 0.668741 0.068611 +All Reads 21 3279 127 23 0.586731 0.052064 +All Reads 22 5106 178 23 0.528099 0.039583 +All Reads 23 7817 319 23 0.618197 0.034612 +All Reads 24 11933 630 24 0.799774 0.031864 +All Reads 25 17449 759 25 0.658943 0.023918 +All Reads 26 25272 1414 26 0.847591 0.02254 +All Reads 27 34926 1806 25 0.783331 0.018433 +All Reads 28 48489 2889 26 0.90257 0.016792 +All Reads 29 64950 4285 26 0.99942 0.015268 +All Reads 30 84452 5453 26 0.978142 0.013246 +All Reads 31 107535 6476 26 0.912291 0.011337 +All Reads 32 134982 7953 26 0.892548 0.010008 +All Reads 33 165941 9475 26 0.864972 0.008886 +All Reads 34 199087 11437 26 0.870253 0.008137 +All Reads 35 233144 12856 26 0.83533 0.007367 +All Reads 36 266049 14918 26 0.849426 0.006955 +All Reads 37 298999 17019 26 0.862265 0.00661 +All Reads 38 327958 20230 26 0.934446 0.00657 +All Reads 39 350801 22684 26 0.97957 0.006504 +All Reads 40 369841 23670 26 0.969527 0.006302 +All Reads 41 383262 25527 26 1.008975 0.006315 +All Reads 42 392470 26131 25 1.008617 0.006239 +All Reads 43 395234 25603 25 0.981326 0.006133 +All Reads 44 392428 26425 25 1.020074 0.006275 +All Reads 45 386569 25213 25 0.988039 0.006222 +All Reads 46 376763 25980 25 1.044594 0.006481 +All Reads 47 363422 24801 25 1.033795 0.006564 +All Reads 48 348339 24838 25 1.080167 0.006854 +All Reads 49 331960 24992 24 1.140491 0.007214 +All Reads 50 315781 23793 24 1.141405 0.0074 +All Reads 51 297249 22601 24 1.151818 0.007662 +All Reads 52 278159 19653 24 1.070317 0.007635 +All Reads 53 263713 19395 24 1.114127 0.008 +All Reads 54 247317 19047 24 1.166673 0.008453 +All Reads 55 230663 17922 23 1.177023 0.008792 +All Reads 56 215458 16244 23 1.142107 0.008961 +All Reads 57 198515 14904 23 1.137329 0.009316 +All Reads 58 180718 13720 23 1.150083 0.009819 +All Reads 59 165914 11940 23 1.090179 0.009977 +All Reads 60 152561 10775 23 1.069917 0.010307 +All Reads 61 138857 9746 23 1.063249 0.01077 +All Reads 62 125804 9067 22 1.091807 0.011466 +All Reads 63 112222 7148 22 0.964902 0.011413 +All Reads 64 99218 6056 23 0.924638 0.011882 +All Reads 65 85414 5612 24 0.995326 0.013286 +All Reads 66 72999 4286 23 0.88943 0.013586 +All Reads 67 61396 3631 23 0.895907 0.014868 +All Reads 68 52109 3341 22 0.971271 0.016804 +All Reads 69 45121 2735 21 0.918238 0.017558 +All Reads 70 38925 1675 21 0.651873 0.015928 +All Reads 71 32225 1053 22 0.495008 0.015254 +All Reads 72 27537 721 22 0.396639 0.014772 +All Reads 73 23481 483 22 0.311607 0.014179 +All Reads 74 20300 423 22 0.315661 0.015348 +All Reads 75 17785 245 22 0.208684 0.013332 +All Reads 76 15846 236 22 0.225615 0.014686 +All Reads 77 13683 230 22 0.254638 0.01679 +All Reads 78 11733 217 23 0.280174 0.019019 +All Reads 79 10547 188 22 0.270026 0.019694 +All Reads 80 9314 151 22 0.245594 0.019986 +All Reads 81 7659 149 23 0.294707 0.024143 +All Reads 82 5813 56 25 0.145937 0.019502 +All Reads 83 4687 46 23 0.148676 0.021921 +All Reads 84 3505 18 23 0.077797 0.018337 +All Reads 85 2385 8 23 0.050813 0.017965 +All Reads 86 1424 5 21 0.053191 0.023788 +All Reads 87 859 3 20 0.052906 0.030545 +All Reads 88 529 0 0 0 0 +All Reads 89 411 0 0 0 0 +All Reads 90 348 0 0 0 0 +All Reads 91 138 0 0 0 0 +All Reads 92 40 0 0 0 0 +All Reads 93 7 0 0 0 0 +All Reads 94 7 0 0 0 0 +All Reads 95 12 0 0 0 0 +All Reads 96 17 0 0 0 0 +All Reads 97 8 0 0 0 0 +All Reads 98 9 0 0 0 0 +All Reads 99 5 0 0 0 0 +All Reads 100 30 0 0 0 0 + + |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/cutadapt.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/cutadapt.txt Thu May 25 17:49:13 2017 -0400 |
| b |
| @@ -0,0 +1,129 @@ +You are running cutadapt 1.6 with Python 2.7.3 +Command line parameters: --format=fastq --anywhere=fakadaptater=CACG --error-rate=0.1 --times=1 --overlap=3 --output=/omaha-beach/cloud_26/files/000/dataset_82.dat /omaha-beach/cloud_26/files/000/dataset_33.dat +Maximum error rate: 10.00% + No. of adapters: 1 + Processed reads: 316390 + Processed bases: 31955390 bp (32.0 Mbp) + Trimmed reads: 68795 (21.7%) + Trimmed bases: 3443775 bp (3.4 Mbp) (10.78% of total) + Too short reads: 0 (0.0% of processed reads) + Too long reads: 0 (0.0% of processed reads) + Total time: 5.28 s + Time per read: 0.017 ms + +=== Adapter 'fakadaptater' === + +Sequence: CACG; Length: 4; Trimmed: 68795 times. +2162 times, it overlapped the 5' end of a read +66633 times, it overlapped the 3' end or was within the read + +No. of allowed errors: +0-4 bp: 0 + +Overview of removed sequences (5') +length count expect max.err error counts +3 357 4943.6 0 357 +4 1805 1235.9 0 1805 + + +Overview of removed sequences (3' or within) +length count expect max.err error counts +3 4175 4943.6 0 4175 +4 520 1235.9 0 520 +5 442 1235.9 0 442 +6 522 1235.9 0 522 +7 538 1235.9 0 538 +8 526 1235.9 0 526 +9 482 1235.9 0 482 +10 547 1235.9 0 547 +11 502 1235.9 0 502 +12 539 1235.9 0 539 +13 571 1235.9 0 571 +14 601 1235.9 0 601 +15 537 1235.9 0 537 +16 592 1235.9 0 592 +17 604 1235.9 0 604 +18 617 1235.9 0 617 +19 594 1235.9 0 594 +20 493 1235.9 0 493 +21 558 1235.9 0 558 +22 503 1235.9 0 503 +23 573 1235.9 0 573 +24 609 1235.9 0 609 +25 653 1235.9 0 653 +26 625 1235.9 0 625 +27 541 1235.9 0 541 +28 501 1235.9 0 501 +29 618 1235.9 0 618 +30 539 1235.9 0 539 +31 614 1235.9 0 614 +32 594 1235.9 0 594 +33 627 1235.9 0 627 +34 572 1235.9 0 572 +35 690 1235.9 0 690 +36 615 1235.9 0 615 +37 654 1235.9 0 654 +38 681 1235.9 0 681 +39 530 1235.9 0 530 +40 731 1235.9 0 731 +41 622 1235.9 0 622 +42 611 1235.9 0 611 +43 722 1235.9 0 722 +44 664 1235.9 0 664 +45 659 1235.9 0 659 +46 651 1235.9 0 651 +47 591 1235.9 0 591 +48 642 1235.9 0 642 +49 545 1235.9 0 545 +50 573 1235.9 0 573 +51 591 1235.9 0 591 +52 567 1235.9 0 567 +53 749 1235.9 0 749 +54 647 1235.9 0 647 +55 753 1235.9 0 753 +56 696 1235.9 0 696 +57 780 1235.9 0 780 +58 607 1235.9 0 607 +59 758 1235.9 0 758 +60 643 1235.9 0 643 +61 578 1235.9 0 578 +62 670 1235.9 0 670 +63 652 1235.9 0 652 +64 816 1235.9 0 816 +65 732 1235.9 0 732 +66 640 1235.9 0 640 +67 644 1235.9 0 644 +68 818 1235.9 0 818 +69 658 1235.9 0 658 +70 587 1235.9 0 587 +71 672 1235.9 0 672 +72 588 1235.9 0 588 +73 645 1235.9 0 645 +74 668 1235.9 0 668 +75 725 1235.9 0 725 +76 651 1235.9 0 651 +77 701 1235.9 0 701 +78 662 1235.9 0 662 +79 655 1235.9 0 655 +80 760 1235.9 0 760 +81 746 1235.9 0 746 +82 705 1235.9 0 705 +83 704 1235.9 0 704 +84 726 1235.9 0 726 +85 692 1235.9 0 692 +86 700 1235.9 0 700 +87 758 1235.9 0 758 +88 640 1235.9 0 640 +89 665 1235.9 0 665 +90 848 1235.9 0 848 +91 693 1235.9 0 693 +92 775 1235.9 0 775 +93 1237 1235.9 0 1237 +94 629 1235.9 0 629 +95 574 1235.9 0 574 +96 525 1235.9 0 525 +97 586 1235.9 0 586 +98 696 1235.9 0 696 +99 860 1235.9 0 860 +100 851 1235.9 0 851 + |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/fastqc_data.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/fastqc_data.txt Thu May 25 17:49:13 2017 -0400 |
| b |
| b'@@ -0,0 +1,2181 @@\n+##FastQC\t0.11.4\n+>>Basic Statistics\tpass\n+#Measure\tValue\n+Filename\tpoulet5_1\n+File type\tConventional base calls\n+Encoding\tSanger / Illumina 1.9\n+Total Sequences\t267849\n+Sequences flagged as poor quality\t0\n+Sequence length\t101\n+%GC\t48\n+>>END_MODULE\n+>>Per base sequence quality\twarn\n+#Base\tMean\tMedian\tLower Quartile\tUpper Quartile\t10th Percentile\t90th Percentile\n+1\t20.91988023102569\t21.0\t21.0\t21.0\t21.0\t21.0\n+2\t20.71684045861661\t21.0\t20.0\t22.0\t19.0\t23.0\n+3\t20.351574954545285\t21.0\t20.0\t21.0\t18.0\t22.0\n+4\t22.531542025544244\t23.0\t22.0\t24.0\t20.0\t24.0\n+5\t24.673566076408722\t25.0\t24.0\t26.0\t24.0\t26.0\n+6\t25.813099918237516\t26.0\t25.0\t27.0\t25.0\t27.0\n+7\t27.587864804423386\t28.0\t27.0\t29.0\t26.0\t29.0\n+8\t27.598941941168345\t28.0\t27.0\t29.0\t26.0\t29.0\n+9\t27.07115949658203\t28.0\t26.0\t28.0\t26.0\t28.0\n+10-11\t27.129873548155864\t28.0\t26.0\t28.0\t25.5\t28.0\n+12-13\t27.009298149330405\t27.5\t26.0\t28.0\t25.5\t28.0\n+14-15\t27.123565889736383\t28.0\t26.5\t28.0\t26.0\t28.0\n+16-17\t27.086309823818645\t28.0\t26.0\t28.0\t26.0\t28.0\n+18-19\t27.07924614241606\t28.0\t26.0\t28.0\t25.5\t28.0\n+20-21\t27.082520375286073\t28.0\t26.0\t28.0\t26.0\t28.0\n+22-23\t27.054301117420636\t28.0\t26.0\t28.0\t25.0\t28.0\n+24-25\t27.06350966402712\t28.0\t26.0\t28.0\t25.0\t28.0\n+26-27\t27.082996389756914\t28.0\t26.0\t28.0\t26.0\t28.0\n+28-29\t27.065495857740743\t28.0\t26.0\t28.0\t25.5\t28.0\n+30-31\t27.09608772106672\t28.0\t26.0\t28.0\t26.0\t28.0\n+32-33\t27.087097581099798\t28.0\t26.0\t28.0\t26.0\t28.0\n+34-35\t27.098251253504774\t28.0\t26.5\t28.0\t26.0\t28.0\n+36-37\t27.05184077595959\t28.0\t26.0\t28.0\t25.5\t28.0\n+38-39\t27.06521958267531\t28.0\t26.0\t28.0\t26.0\t28.0\n+40-41\t27.072148859992012\t28.0\t26.0\t28.0\t26.0\t28.0\n+42-43\t27.065725464720796\t28.0\t26.0\t28.0\t25.5\t28.0\n+44-45\t27.07168031241483\t28.0\t26.5\t28.0\t25.5\t28.0\n+46-47\t27.048083061725073\t28.0\t26.0\t28.0\t25.5\t28.0\n+48-49\t27.04642354460909\t28.0\t26.0\t28.0\t25.5\t28.0\n+50-51\t27.062865644448927\t28.0\t26.0\t28.0\t25.5\t28.0\n+52-53\t27.01859629866081\t28.0\t26.0\t28.0\t25.0\t28.0\n+54-55\t26.994157155710866\t27.5\t26.0\t28.0\t25.0\t28.0\n+56-57\t27.110127347871376\t28.0\t27.0\t28.0\t26.0\t28.0\n+58-59\t26.995846540401494\t27.5\t26.0\t28.0\t25.0\t28.0\n+60-61\t27.00461640700544\t27.5\t26.0\t28.0\t25.0\t28.0\n+62-63\t26.981614641085088\t27.5\t26.5\t28.0\t25.5\t28.5\n+64-65\t26.98900313236189\t28.0\t26.0\t28.0\t25.0\t28.0\n+66-67\t27.001189102815392\t28.0\t26.0\t28.0\t25.0\t28.0\n+68-69\t26.917739099268616\t27.5\t26.0\t28.0\t25.0\t28.5\n+70-71\t26.98481793846533\t28.0\t27.0\t28.0\t25.0\t29.0\n+72-73\t26.89518908041471\t27.5\t26.5\t28.0\t25.0\t28.5\n+74-75\t26.93677034448514\t28.0\t27.0\t28.0\t25.0\t29.0\n+76-77\t26.87640237596556\t28.0\t26.5\t28.0\t25.0\t29.0\n+78-79\t26.906094478605482\t28.0\t27.0\t28.0\t25.0\t29.0\n+80-81\t26.80463992772047\t28.0\t26.5\t28.0\t25.0\t29.0\n+82-83\t26.717012197170796\t28.0\t26.5\t28.0\t25.0\t29.0\n+84-85\t26.46960974280285\t27.5\t26.5\t28.0\t25.0\t29.0\n+86-87\t26.442842795754324\t27.5\t26.5\t28.0\t25.0\t29.0\n+88-89\t26.34282375517549\t28.0\t26.0\t28.0\t25.0\t29.0\n+90-91\t26.03493946215965\t28.0\t26.0\t28.0\t24.5\t29.0\n+92-93\t25.833215729758187\t28.0\t26.0\t28.0\t24.0\t29.0\n+94-95\t25.503102494315826\t27.5\t26.0\t28.0\t22.5\t29.0\n+96-97\t24.52807178671565\t27.0\t25.5\t27.5\t21.0\t28.0\n+98-99\t23.202399486277717\t26.0\t24.5\t26.5\t10.0\t27.0\n+100-101\t23.72906749698524\t27.0\t26.0\t28.0\t2.0\t29.0\n+>>END_MODULE\n+>>Per tile sequence quality\tpass\n+#Tile\tBase\tMean\n+1101\t1\t0.017259946109469126\n+1101\t2\t-0.13408255940416325\n+1101\t3\t-0.11853598095770224\n+1101\t4\t0.015421063929771606\n+1101\t5\t-0.06886052494072459\n+1101\t6\t-0.15241701542762698\n+1101\t7\t-0.029853727500473326\n+1101\t8\t0.04533865186875374\n+1101\t9\t0.07102084333114078\n+1101\t10-11\t0.02726717483210095\n+1101\t12-13\t0.05147474989913192\n+1101\t14-15\t-0.006227419450461014\n+1101\t16-17\t0.051879075943595865\n+1101\t18-19\t0.03525737425918152\n+1101\t20-21\t0.012963832365290529\n+1101\t22-23\t0.02506089814612622\n+1101\t24-25\t0.07843149833360386\n+1101\t26-27\t0.02737786083297422\n+1101\t28-29\t0.005161107012540356\n+1101\t30-31\t-0.08720467946375265\n+1101\t32-33\t-0.017197404032327057\n+1101\t34-35\t0.05763469947927646\n+1101\t36-37\t-0.045600552109540615\n+1101\t38-39\t-0.01952943529413176\n+1101\t40-41\t0.007678874836642535\n+1101\t42-43\t-0.00844'..b'433.5\n+55\t9922.0\n+56\t8785.5\n+57\t7997.0\n+58\t6901.0\n+59\t5796.0\n+60\t4967.0\n+61\t4072.5\n+62\t3639.5\n+63\t3267.0\n+64\t2561.5\n+65\t2002.5\n+66\t1561.5\n+67\t1355.5\n+68\t1222.0\n+69\t1019.0\n+70\t803.0\n+71\t568.5\n+72\t371.5\n+73\t235.0\n+74\t164.5\n+75\t110.5\n+76\t70.5\n+77\t56.0\n+78\t39.5\n+79\t27.0\n+80\t18.0\n+81\t17.0\n+82\t15.5\n+83\t12.5\n+84\t6.5\n+85\t1.5\n+86\t0.0\n+87\t0.0\n+88\t0.0\n+89\t0.0\n+90\t0.0\n+91\t0.0\n+92\t0.0\n+93\t0.0\n+94\t0.0\n+95\t0.0\n+96\t0.0\n+97\t0.0\n+98\t0.0\n+99\t0.0\n+100\t0.0\n+>>END_MODULE\n+>>Per base N content\tpass\n+#Base\tN-Count\n+1\t0.029867574640935753\n+2\t0.0\n+3\t0.003733446830116969\n+4\t0.0\n+5\t3.733446830116969E-4\n+6\t0.0\n+7\t0.0\n+8\t0.0\n+9\t0.0\n+10-11\t0.0\n+12-13\t0.0\n+14-15\t0.0\n+16-17\t0.0\n+18-19\t0.0\n+20-21\t0.0\n+22-23\t0.0\n+24-25\t0.0\n+26-27\t0.0\n+28-29\t0.0\n+30-31\t0.0\n+32-33\t0.0\n+34-35\t0.0\n+36-37\t0.0\n+38-39\t0.0\n+40-41\t0.0\n+42-43\t0.0\n+44-45\t0.0\n+46-47\t0.0\n+48-49\t0.0\n+50-51\t0.0\n+52-53\t0.0\n+54-55\t0.0\n+56-57\t0.0\n+58-59\t0.0\n+60-61\t0.0\n+62-63\t0.0\n+64-65\t0.0\n+66-67\t0.0\n+68-69\t0.0\n+70-71\t0.0\n+72-73\t0.0\n+74-75\t0.0\n+76-77\t0.0\n+78-79\t0.0\n+80-81\t0.0\n+82-83\t0.0\n+84-85\t0.0\n+86-87\t0.0\n+88-89\t0.0\n+90-91\t0.0\n+92-93\t0.0\n+94-95\t0.0\n+96-97\t0.0\n+98-99\t0.0\n+100-101\t0.0\n+>>END_MODULE\n+>>Sequence Length Distribution\tpass\n+#Length\tCount\n+101\t267849.0\n+>>END_MODULE\n+>>Sequence Duplication Levels\twarn\n+#Total Deduplicated Percentage\t63.69408840068983\n+#Duplication Level\tPercentage of deduplicated\tPercentage of total\n+1\t81.5623716290639\t51.950409087115126\n+2\t9.995611185249079\t12.733226849043577\n+3\t3.1947144335386772\t6.104532706343167\n+4\t1.4905270052149588\t3.797510353351082\n+5\t0.8725392208870194\t2.778779513412342\n+6\t0.55360835935223\t2.115694786796508\n+7\t0.38537193434967776\t1.718213983752925\n+8\t0.314619574221819\t1.603152557845755\n+9\t0.2033036957962869\t1.1654319215012086\n+>10\t1.4223398099582591\t15.850860027094066\n+>50\t0.0049931523680946535\t0.18218821374420768\n+>100\t0.0\t0.0\n+>500\t0.0\t0.0\n+>1k\t0.0\t0.0\n+>5k\t0.0\t0.0\n+>10k+\t0.0\t0.0\n+>>END_MODULE\n+>>Overrepresented sequences\tpass\n+>>END_MODULE\n+>>Adapter Content\tpass\n+#Position\tIllumina Universal Adapter\tIllumina Small RNA Adapter\tNextera Transposase Sequence\tSOLID Small RNA Adapter\n+1\t0.0\t0.0\t0.0\t0.0\n+2\t0.0\t0.0\t0.0\t0.0\n+3\t0.0\t0.0\t0.0\t0.0\n+4\t0.0\t0.0\t0.0\t0.0\n+5\t0.0\t0.0\t0.0\t0.0\n+6\t0.0\t0.0\t0.0\t0.0\n+7\t0.0\t0.0\t0.0\t0.0\n+8\t0.0\t0.0\t0.0\t0.0\n+9\t0.0\t0.0\t0.0\t0.0\n+10-11\t0.0\t0.0\t0.0\t0.0\n+12-13\t0.0\t0.0\t0.0\t0.0\n+14-15\t0.0\t0.0\t0.0\t0.0\n+16-17\t0.0\t0.0\t0.0\t0.0\n+18-19\t0.0\t0.0\t0.0\t0.0\n+20-21\t0.0\t0.0\t0.0\t0.0\n+22-23\t0.0\t0.0\t0.0\t0.0\n+24-25\t0.0\t0.0\t0.0\t0.0\n+26-27\t0.0\t0.0\t0.0\t0.0\n+28-29\t0.0\t0.0\t0.0\t0.0\n+30-31\t0.0\t0.0\t0.0\t0.0\n+32-33\t0.0\t0.0\t0.0\t0.0\n+34-35\t0.0\t0.0\t0.0\t0.0\n+36-37\t0.0\t0.0\t0.0\t0.0\n+38-39\t0.0\t0.0\t0.0\t0.0\n+40-41\t0.0\t0.0\t0.0\t0.0\n+42-43\t0.0\t0.0\t0.0\t0.0\n+44-45\t0.0\t0.0\t0.0\t0.0\n+46-47\t0.0\t0.0\t0.0\t0.0\n+48-49\t0.0\t0.0\t0.0\t0.0\n+50-51\t0.0\t0.0\t0.0\t0.0\n+52-53\t0.0\t0.0\t0.0\t0.0\n+54-55\t0.0\t0.0\t0.0\t0.0\n+56-57\t0.0\t0.0\t0.0\t0.0\n+58-59\t0.0\t0.0\t0.0\t0.0\n+60-61\t0.0\t0.0\t0.0\t0.0\n+62-63\t0.0\t0.0\t0.0\t0.0\n+64-65\t0.0\t0.0\t0.0\t0.0\n+66-67\t0.0\t0.0\t0.0\t0.0\n+68-69\t0.0\t0.0\t0.0\t0.0\n+70-71\t0.0\t0.0\t0.0\t0.0\n+72-73\t0.0\t0.0\t0.0\t0.0\n+74-75\t0.0\t0.0\t0.0\t0.0\n+76-77\t0.0\t0.0\t0.0\t0.0\n+78-79\t0.0\t0.0\t0.0\t0.0\n+80-81\t0.0\t0.0\t0.0\t0.0\n+82-83\t0.0\t0.0\t0.0\t0.0\n+84-85\t0.0\t0.0\t0.0\t0.0\n+86-87\t0.0\t0.0\t0.0\t0.0\n+88-89\t0.0\t0.0\t0.0\t0.0\n+>>END_MODULE\n+>>Kmer Content\twarn\n+#Sequence\tCount\tPValue\tObs/Exp Max\tMax Obs/Exp Position\n+TTAGTGG\t50\t0.0016122013\t38.00672\t3\n+CCGGGAA\t65\t0.0058204937\t29.246862\t1\n+CTCGCCA\t65\t0.0058204937\t29.246862\t1\n+CCCGCTT\t70\t0.008357804\t27.157803\t1\n+AACAATT\t125\t0.006013185\t19.00336\t2\n+CTGGGAT\t205\t3.3062082E-4\t16.228443\t1\n+AGTTCAA\t195\t0.0044498937\t14.615241\t5\n+GAGTAGT\t125\t0.0014974214\t13.29987\t30-31\n+AAGTTCA\t220\t0.009890434\t12.954418\t4\n+CTGAAAT\t275\t0.003044474\t12.097567\t1\n+CCCAGCT\t405\t3.2130985E-5\t11.734852\t1\n+AGGGTGT\t145\t0.0045575905\t11.465405\t66-67\n+CTGAATT\t335\t0.001024679\t11.349529\t1\n+CTTGAAT\t295\t0.0051441877\t11.277392\t1\n+GAATGTC\t425\t6.555659E-4\t10.058724\t4\n+GGTAGTA\t190\t0.002949709\t9.999902\t52-53\n+CTCTGCC\t390\t0.0036302158\t9.748955\t1\n+CTCCTTT\t535\t5.356131E-4\t8.883393\t1\n+CTTTGCT\t500\t0.0028739348\t8.5547085\t1\n+>>END_MODULE\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/fastqc_data_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/fastqc_data_2.txt Thu May 25 17:49:13 2017 -0400 |
| b |
| b'@@ -0,0 +1,2170 @@\n+##FastQC\t0.11.4\n+>>Basic Statistics\tpass\n+#Measure\tValue\n+Filename\tpoulet5_2\n+File type\tConventional base calls\n+Encoding\tSanger / Illumina 1.9\n+Total Sequences\t267849\n+Sequences flagged as poor quality\t0\n+Sequence length\t101\n+%GC\t48\n+>>END_MODULE\n+>>Per base sequence quality\twarn\n+#Base\tMean\tMedian\tLower Quartile\tUpper Quartile\t10th Percentile\t90th Percentile\n+1\t20.590586487162543\t21.0\t21.0\t21.0\t20.0\t21.0\n+2\t20.458478471078855\t21.0\t19.0\t22.0\t19.0\t22.0\n+3\t20.178608096352797\t21.0\t20.0\t21.0\t18.0\t22.0\n+4\t22.495204387546714\t23.0\t22.0\t24.0\t20.0\t24.0\n+5\t24.59397272343746\t25.0\t24.0\t26.0\t24.0\t26.0\n+6\t25.77560491172265\t26.0\t25.0\t27.0\t25.0\t27.0\n+7\t26.651378201897337\t27.0\t26.0\t28.0\t26.0\t28.0\n+8\t27.54968284369178\t28.0\t27.0\t29.0\t26.0\t29.0\n+9\t27.089005372429988\t28.0\t26.0\t28.0\t26.0\t28.0\n+10-11\t27.058984726469017\t28.0\t26.0\t28.0\t25.5\t28.0\n+12-13\t26.954911162632676\t27.5\t26.0\t28.0\t25.5\t28.0\n+14-15\t27.066410552214123\t28.0\t26.0\t28.0\t26.0\t28.0\n+16-17\t27.04552938409328\t28.0\t26.0\t28.0\t25.5\t28.0\n+18-19\t27.025118630273028\t28.0\t26.0\t28.0\t25.0\t28.0\n+20-21\t27.019042445557012\t28.0\t26.0\t28.0\t25.0\t28.0\n+22-23\t27.010315513591614\t28.0\t26.0\t28.0\t25.0\t28.0\n+24-25\t27.03931879529138\t28.0\t26.0\t28.0\t25.5\t28.0\n+26-27\t26.978450544896567\t28.0\t26.0\t28.0\t25.0\t28.0\n+28-29\t27.003714779595967\t28.0\t26.0\t28.0\t25.0\t28.0\n+30-31\t27.025971722873706\t28.0\t26.0\t28.0\t25.0\t28.0\n+32-33\t27.017791740868923\t28.0\t26.0\t28.0\t25.0\t28.0\n+34-35\t27.00628899118533\t28.0\t26.0\t28.0\t25.0\t28.0\n+36-37\t27.00906294218011\t28.0\t26.0\t28.0\t25.0\t28.0\n+38-39\t27.034922661648913\t28.0\t26.0\t28.0\t25.5\t28.0\n+40-41\t27.005346295860726\t28.0\t26.0\t28.0\t25.0\t28.0\n+42-43\t27.000909094303132\t28.0\t26.0\t28.0\t25.0\t28.0\n+44-45\t27.004913216028434\t28.0\t26.0\t28.0\t25.0\t28.0\n+46-47\t26.979999925331065\t28.0\t26.0\t28.0\t25.0\t28.0\n+48-49\t26.941037674211962\t27.5\t26.0\t28.0\t25.0\t28.0\n+50-51\t26.99995146519121\t27.5\t26.0\t28.0\t25.5\t28.0\n+52-53\t26.95084543903468\t27.5\t26.0\t28.0\t25.0\t28.0\n+54-55\t26.97609847339359\t28.0\t26.0\t28.0\t25.0\t28.0\n+56-57\t26.99262270906369\t27.5\t26.0\t28.0\t25.0\t28.0\n+58-59\t26.942271578389317\t27.0\t26.0\t28.0\t25.0\t28.0\n+60-61\t26.88024222603034\t27.0\t26.0\t28.0\t25.0\t28.0\n+62-63\t26.866450873439888\t27.0\t26.0\t28.0\t25.0\t28.0\n+64-65\t26.947610407356386\t28.0\t26.0\t28.0\t25.0\t28.0\n+66-67\t26.975012040366025\t28.0\t26.5\t28.0\t25.0\t28.5\n+68-69\t26.966286975124042\t28.0\t26.5\t28.0\t25.0\t29.0\n+70-71\t26.917634562757375\t28.0\t26.0\t28.0\t25.0\t29.0\n+72-73\t26.885127441207544\t28.0\t26.0\t28.0\t25.0\t29.0\n+74-75\t26.846286527110426\t28.0\t26.5\t28.0\t25.0\t29.0\n+76-77\t26.769134848366058\t28.0\t26.0\t28.0\t25.0\t29.0\n+78-79\t26.709703975000842\t28.0\t26.5\t28.0\t25.0\t29.0\n+80-81\t26.551336760637525\t27.5\t26.0\t28.0\t25.0\t28.5\n+82-83\t26.42626069165836\t27.5\t26.0\t28.0\t25.0\t28.5\n+84-85\t26.309463541024982\t27.5\t26.0\t28.0\t25.0\t29.0\n+86-87\t26.127226534353312\t27.5\t26.0\t28.0\t25.0\t29.0\n+88-89\t25.91885539987082\t27.5\t26.0\t28.0\t24.0\t29.0\n+90-91\t25.674260497519125\t27.0\t26.0\t28.0\t23.5\t29.0\n+92-93\t25.371903572535274\t27.0\t26.0\t28.0\t22.0\t29.0\n+94-95\t24.758753999454918\t27.0\t26.0\t28.0\t20.5\t28.5\n+96-97\t23.84710415196622\t26.5\t25.0\t27.5\t7.0\t28.0\n+98-99\t22.40618968149965\t25.5\t24.0\t26.5\t2.0\t27.0\n+100-101\t23.009550156991438\t27.0\t25.0\t28.0\t2.0\t29.0\n+>>END_MODULE\n+>>Per tile sequence quality\tpass\n+#Tile\tBase\tMean\n+1101\t1\t-0.1408369887985721\n+1101\t2\t-0.019030947201084558\n+1101\t3\t-0.060059442415557385\n+1101\t4\t0.004085939732711097\n+1101\t5\t-0.018429270835582656\n+1101\t6\t-0.10404524639907464\n+1101\t7\t0.05541229462318498\n+1101\t8\t0.06703529503928962\n+1101\t9\t0.0644374620344621\n+1101\t10-11\t0.06977859906234585\n+1101\t12-13\t0.048103685880093394\n+1101\t14-15\t0.0848396420659725\n+1101\t16-17\t0.030233298636137107\n+1101\t18-19\t0.05253119669850648\n+1101\t20-21\t0.08961672433820667\n+1101\t22-23\t0.014190195653434046\n+1101\t24-25\t-0.013817302849609803\n+1101\t26-27\t0.046003756870838686\n+1101\t28-29\t0.04599618351544166\n+1101\t30-31\t0.04851104267937956\n+1101\t32-33\t0.04656194043190354\n+1101\t34-35\t0.057517795385400916\n+1101\t36-37\t-0.00326392946157128\n+1101\t38-39\t0.0753296536157606\n+1101\t40-41\t0.005995075411309614\n+1101\t42-43\t-0.013913'..b'71.0\n+24\t130.0\n+25\t233.5\n+26\t389.5\n+27\t542.5\n+28\t724.5\n+29\t1063.0\n+30\t1433.0\n+31\t1683.5\n+32\t1996.0\n+33\t2367.5\n+34\t2840.5\n+35\t3318.0\n+36\t3924.5\n+37\t4721.0\n+38\t5510.0\n+39\t6259.0\n+40\t7364.0\n+41\t8736.0\n+42\t9608.5\n+43\t10256.0\n+44\t10928.5\n+45\t11153.5\n+46\t11271.5\n+47\t12042.0\n+48\t12804.5\n+49\t12874.0\n+50\t12482.5\n+51\t11758.0\n+52\t10827.0\n+53\t10433.0\n+54\t10615.0\n+55\t9955.0\n+56\t8760.0\n+57\t7986.5\n+58\t6982.5\n+59\t5802.5\n+60\t4913.5\n+61\t4177.5\n+62\t3751.5\n+63\t3282.0\n+64\t2533.0\n+65\t1954.0\n+66\t1513.0\n+67\t1247.5\n+68\t1102.0\n+69\t957.0\n+70\t777.0\n+71\t535.5\n+72\t361.5\n+73\t253.0\n+74\t157.0\n+75\t99.0\n+76\t60.0\n+77\t46.5\n+78\t37.0\n+79\t21.5\n+80\t13.5\n+81\t16.5\n+82\t19.5\n+83\t14.0\n+84\t6.5\n+85\t3.0\n+86\t0.5\n+87\t0.0\n+88\t0.0\n+89\t0.0\n+90\t0.0\n+91\t0.0\n+92\t0.0\n+93\t0.0\n+94\t0.0\n+95\t0.0\n+96\t0.0\n+97\t0.0\n+98\t0.0\n+99\t0.0\n+100\t0.0\n+>>END_MODULE\n+>>Per base N content\tpass\n+#Base\tN-Count\n+1\t0.11461681768459094\n+2\t0.003733446830116969\n+3\t0.0\n+4\t0.0\n+5\t0.0\n+6\t0.0\n+7\t0.0\n+8\t0.0\n+9\t0.0\n+10-11\t0.0\n+12-13\t0.0\n+14-15\t0.0\n+16-17\t0.0\n+18-19\t0.0\n+20-21\t0.0\n+22-23\t0.0\n+24-25\t0.0\n+26-27\t0.0\n+28-29\t0.0\n+30-31\t0.0\n+32-33\t0.0\n+34-35\t0.0\n+36-37\t0.0\n+38-39\t0.0\n+40-41\t0.0\n+42-43\t0.0\n+44-45\t0.0\n+46-47\t0.0\n+48-49\t0.0\n+50-51\t0.0\n+52-53\t0.0\n+54-55\t0.0\n+56-57\t0.0\n+58-59\t0.0\n+60-61\t0.0\n+62-63\t0.0\n+64-65\t0.0\n+66-67\t0.0\n+68-69\t0.0\n+70-71\t0.0\n+72-73\t0.0\n+74-75\t0.0\n+76-77\t0.0\n+78-79\t0.0\n+80-81\t0.0\n+82-83\t1.8667234150584845E-4\n+84-85\t0.0\n+86-87\t1.8667234150584845E-4\n+88-89\t0.0014933787320467876\n+90-91\t0.0\n+92-93\t0.0011200340490350907\n+94-95\t0.0\n+96-97\t0.0\n+98-99\t0.0\n+100-101\t0.01456044263745618\n+>>END_MODULE\n+>>Sequence Length Distribution\tpass\n+#Length\tCount\n+101\t267849.0\n+>>END_MODULE\n+>>Sequence Duplication Levels\twarn\n+#Total Deduplicated Percentage\t63.826611251945884\n+#Duplication Level\tPercentage of deduplicated\tPercentage of total\n+1\t81.66283073871745\t52.122617512935754\n+2\t9.894108596885154\t12.630148461958491\n+3\t3.18062640137576\t6.090258145748586\n+4\t1.5566170090070461\t3.974143548082379\n+5\t0.8538567368205473\t2.7249391002950074\n+6\t0.5533319107768025\t2.119038045746843\n+7\t0.3960736941041749\t1.7696029190496514\n+8\t0.2698969625036296\t1.3781286803040145\n+9\t0.23212846037984958\t1.3334375701059644\n+>10\t1.3969694370078172\t15.730893862039416\n+>50\t0.0035600524217624095\t0.12679215373389083\n+>100\t0.0\t0.0\n+>500\t0.0\t0.0\n+>1k\t0.0\t0.0\n+>5k\t0.0\t0.0\n+>10k+\t0.0\t0.0\n+>>END_MODULE\n+>>Overrepresented sequences\tpass\n+>>END_MODULE\n+>>Adapter Content\tpass\n+#Position\tIllumina Universal Adapter\tIllumina Small RNA Adapter\tNextera Transposase Sequence\tSOLID Small RNA Adapter\n+1\t0.0\t0.0\t0.0\t0.0\n+2\t0.0\t0.0\t0.0\t0.0\n+3\t0.0\t0.0\t0.0\t0.0\n+4\t0.0\t0.0\t0.0\t0.0\n+5\t0.0\t0.0\t0.0\t0.0\n+6\t0.0\t0.0\t0.0\t0.0\n+7\t0.0\t0.0\t0.0\t0.0\n+8\t0.0\t0.0\t0.0\t0.0\n+9\t0.0\t0.0\t0.0\t0.0\n+10-11\t0.0\t0.0\t0.0\t0.0\n+12-13\t0.0\t0.0\t0.0\t0.0\n+14-15\t0.0\t0.0\t0.0\t0.0\n+16-17\t0.0\t0.0\t0.0\t0.0\n+18-19\t0.0\t0.0\t0.0\t0.0\n+20-21\t0.0\t0.0\t0.0\t0.0\n+22-23\t0.0\t0.0\t0.0\t0.0\n+24-25\t0.0\t0.0\t0.0\t0.0\n+26-27\t0.0\t0.0\t0.0\t0.0\n+28-29\t0.0\t0.0\t0.0\t0.0\n+30-31\t0.0\t0.0\t0.0\t0.0\n+32-33\t0.0\t0.0\t0.0\t0.0\n+34-35\t0.0\t0.0\t0.0\t0.0\n+36-37\t0.0\t0.0\t0.0\t0.0\n+38-39\t0.0\t0.0\t0.0\t0.0\n+40-41\t0.0\t0.0\t0.0\t0.0\n+42-43\t0.0\t0.0\t0.0\t0.0\n+44-45\t0.0\t0.0\t0.0\t0.0\n+46-47\t0.0\t0.0\t0.0\t0.0\n+48-49\t0.0\t0.0\t0.0\t0.0\n+50-51\t0.0\t0.0\t0.0\t0.0\n+52-53\t0.0\t0.0\t0.0\t0.0\n+54-55\t0.0\t0.0\t0.0\t0.0\n+56-57\t0.0\t0.0\t0.0\t0.0\n+58-59\t0.0\t0.0\t0.0\t0.0\n+60-61\t0.0\t0.0\t0.0\t0.0\n+62-63\t0.0\t0.0\t0.0\t0.0\n+64-65\t0.0\t0.0\t0.0\t0.0\n+66-67\t0.0\t0.0\t0.0\t0.0\n+68-69\t0.0\t0.0\t0.0\t0.0\n+70-71\t0.0\t0.0\t0.0\t0.0\n+72-73\t0.0\t0.0\t0.0\t0.0\n+74-75\t0.0\t0.0\t0.0\t0.0\n+76-77\t0.0\t0.0\t0.0\t0.0\n+78-79\t0.0\t0.0\t0.0\t0.0\n+80-81\t0.0\t0.0\t0.0\t0.0\n+82-83\t0.0\t0.0\t0.0\t0.0\n+84-85\t0.0\t0.0\t0.0\t0.0\n+86-87\t0.0\t0.0\t0.0\t0.0\n+88-89\t0.0\t0.0\t0.0\t0.0\n+>>END_MODULE\n+>>Kmer Content\twarn\n+#Sequence\tCount\tPValue\tObs/Exp Max\tMax Obs/Exp Position\n+TACGAGG\t60\t0.0039460836\t31.665857\t9\n+CCCAGAT\t105\t6.861368E-5\t27.157375\t1\n+AATCAAC\t70\t0.008381328\t27.142164\t5\n+CTTGTAT\t120\t0.004739449\t19.802252\t1\n+TCGCTCA\t130\t0.007549489\t18.268764\t2\n+CCCCACT\t195\t0.0044338168\t14.623201\t1\n+TTCAACA\t295\t0.005166332\t11.270898\t2\n+CTTGAAG\t305\t0.006593838\t10.90747\t1\n+>>END_MODULE\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/featurecounts_data.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/featurecounts_data.txt Thu May 25 17:49:13 2017 -0400 |
| b |
| @@ -0,0 +1,12 @@ +Status 70: TopHat on data 1, data 4, and data 3: accepted_hits 75: TopHat on data 1, data 6, and data 5: accepted_hits 80: TopHat on data 1, data 8, and data 7: accepted_hits 85: TopHat on data 1, data 10, and data 9: accepted_hits 90: TopHat on data 1, data 12, and data 11: accepted_hits 95: TopHat on data 1, data 14, and data 13: accepted_hits +Assigned 321797 445012 394981 437485 388170 453929 +Unassigned_Ambiguity 2333 3424 3121 3692 2782 3554 +Unassigned_MultiMapping 19123 25293 22580 19907 21164 23533 +Unassigned_NoFeatures 111117 165786 129664 146327 132063 160805 +Unassigned_Unmapped 0 0 0 0 0 0 +Unassigned_MappingQuality 0 0 0 0 0 0 +Unassigned_FragmentLength 0 0 0 0 0 0 +Unassigned_Chimera 0 0 0 0 0 0 +Unassigned_Secondary 0 0 0 0 0 0 +Unassigned_Nonjunction 0 0 0 0 0 0 +Unassigned_Duplicate 0 0 0 0 0 0 |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/htseq_data.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/htseq_data.txt Thu May 25 17:49:13 2017 -0400 |
| b |
| @@ -0,0 +1,5 @@ +__no_feature 19 +__ambiguous 0 +__too_low_aQual 0 +__not_aligned 1336 +__alignment_not_unique 0 |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/log_fastqc.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/log_fastqc.txt Thu May 25 17:49:13 2017 -0400 |
| [ |
| b"@@ -0,0 +1,57 @@\n+[2017-05-25 01:09:17,435] multiqc [DEBUG ] No MultiQC config found: /home/dpryan/miniconda2/lib/python2.7/site-packages/multiqc-1.0-py2.7.egg/multiqc_config.yaml\n+[2017-05-25 01:09:17,435] multiqc [DEBUG ] No MultiQC config found: /home/dpryan/.multiqc_config.yaml\n+[2017-05-25 01:09:17,435] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml\n+[2017-05-25 01:09:17,435] multiqc [DEBUG ] Command used: /home/dpryan/miniconda2/bin/multiqc multiqc_WDir\n+[2017-05-25 01:09:17,435] multiqc [DEBUG ] Could not connect to multiqc.info for version check\n+[2017-05-25 01:09:17,435] multiqc [INFO ] This is MultiQC v1.0\n+[2017-05-25 01:09:17,435] multiqc [DEBUG ] Command : /home/dpryan/miniconda2/bin/multiqc multiqc_WDir\n+[2017-05-25 01:09:17,435] multiqc [DEBUG ] Working dir : /tmp/tmptvpHhR/job_working_directory/000/2/working\n+[2017-05-25 01:09:17,435] multiqc [INFO ] Template : default\n+[2017-05-25 01:09:17,436] multiqc [INFO ] Searching 'multiqc_WDir'\n+[2017-05-25 01:09:17,436] multiqc [DEBUG ] Analysing modules: custom_content, peddy, methylQA, qualimap, preseq, quast, rna_seqc, rseqc, busco, goleft_indexcov, snpeff, gatk, htseq, bcftools, featureCounts, picard, prokka, samblaster, samtools, bamtools, bismark, hicup, salmon, kallisto, slamdunk, star, tophat, bowtie2, bowtie1, adapterRemoval, cutadapt, trimmomatic, skewer, sortmerna, fastq_screen, fastqc, clusterflow\n+[2017-05-25 01:09:17,436] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmpExYq9v\n+[2017-05-25 01:09:17,570] multiqc.modules.custom_content.custom_content [DEBUG ] No custom content found\n+[2017-05-25 01:09:17,573] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,576] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,578] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50\n+[2017-05-25 01:09:17,579] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,581] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,584] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,586] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,589] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,591] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,594] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,596] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,598] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,601] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,6"..b",)\n+[2017-05-25 01:09:17,611] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,614] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,617] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,619] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,621] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,624] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,626] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,629] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,631] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found.\n+[2017-05-25 01:09:17,633] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,636] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,638] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,641] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,643] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,645] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,648] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,650] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,652] multiqc.modules.sortmerna.sortmerna [DEBUG ] Could not find any SortMeRNA data in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,655] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,694] multiqc.modules.fastqc.fastqc [INFO ] Found 1 reports\n+[2017-05-25 01:09:17,748] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-05-25 01:09:17,750] multiqc [INFO ] Compressing plot data\n+[2017-05-25 01:09:17,802] multiqc [INFO ] Report : multiqc_report.html\n+[2017-05-25 01:09:17,802] multiqc [INFO ] Data : multiqc_data\n+[2017-05-25 01:09:17,802] multiqc [DEBUG ] Moving data file from '/tmp/tmpExYq9v/multiqc_data/multiqc_general_stats.txt' to '/tmp/tmptvpHhR/job_working_directory/000/2/working/multiqc_data'\n+[2017-05-25 01:09:17,803] multiqc [DEBUG ] Moving data file from '/tmp/tmpExYq9v/multiqc_data/multiqc_fastqc.txt' to '/tmp/tmptvpHhR/job_working_directory/000/2/working/multiqc_data'\n+[2017-05-25 01:09:17,803] multiqc [DEBUG ] Moving data file from '/tmp/tmpExYq9v/multiqc_data/multiqc_sources.txt' to '/tmp/tmptvpHhR/job_working_directory/000/2/working/multiqc_data'\n+[2017-05-25 01:09:17,900] multiqc [INFO ] MultiQC complete\n" |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/picard_CollectAlignmentSummaryMetrics.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/picard_CollectAlignmentSummaryMetrics.txt Thu May 25 17:49:13 2017 -0400 |
| [ |
| @@ -0,0 +1,10 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false REFERENCE_SEQUENCE=/data/repository/organisms/GRCm38_ensembl/genome_fasta/genome.fa INPUT=D11_H4K16ac_Rep1_R1_fastq_gz OUTPUT=/data/galaxy2/files/000/163/dataset_163662.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json +## htsjdk.samtools.metrics.StringHeader +# Started on: Fri Apr 21 14:00:55 CEST 2017 + +## METRICS CLASS picard.analysis.AlignmentSummaryMetrics +CATEGORY TOTAL_READS PF_READS PCT_PF_READS PF_NOISE_READS PF_READS_ALIGNED PCT_PF_READS_ALIGNED PF_ALIGNED_BASES PF_HQ_ALIGNED_READS PF_HQ_ALIGNED_BASES PF_HQ_ALIGNED_Q20_BASES PF_HQ_MEDIAN_MISMATCHES PF_MISMATCH_RATE PF_HQ_ERROR_RATE PF_INDEL_RATE MEAN_READ_LENGTH READS_ALIGNED_IN_PAIRS PCT_READS_ALIGNED_IN_PAIRS BAD_CYCLES STRAND_BALANCE PCT_CHIMERAS PCT_ADAPTER SAMPLE LIBRARY READ_GROUP +UNPAIRED 16199126 16199126 1 112 15925118 0.983085 1189439864 11288718 843872901 802235299 0 0.011597 0.006165 0.000848 74.733459 0 0 0 0.494061 0 0.000014 + + |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/picard_CollectBaseDistributionByCycle.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/picard_CollectBaseDistributionByCycle.txt Thu May 25 17:49:13 2017 -0400 |
| b |
| @@ -0,0 +1,84 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.analysis.CollectBaseDistributionByCycle CHART_OUTPUT=/data/galaxy2/files/000/163/dataset_163657.dat ALIGNED_READS_ONLY=true PF_READS_ONLY=true INPUT=D11_H4K16ac_Rep1_R1_fastq_gz OUTPUT=/data/galaxy2/files/000/163/dataset_163656.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=/data/repository/organisms/GRCm38_ensembl/genome_fasta/genome.fa STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json +## htsjdk.samtools.metrics.StringHeader +# Started on: Fri Apr 21 13:59:56 CEST 2017 + +## METRICS CLASS picard.analysis.BaseDistributionByCycleMetrics +READ_END CYCLE PCT_A PCT_C PCT_G PCT_T PCT_N +1 1 45.534532 6.100294 6.278409 41.942176 0.144589 +1 2 18.642016 31.079914 32.291905 17.974837 0.011328 +1 3 25.118841 24.321879 26.15791 24.401106 0.000264 +1 4 22.612561 27.464826 27.30928 22.606024 0.007309 +1 5 27.970543 22.96859 21.970694 27.090173 0 +1 6 28.405874 22.976144 21.741647 26.875952 0.000383 +1 7 31.150444 19.648545 20.094438 29.10656 0.000013 +1 8 31.215988 19.341113 20.496087 28.946812 0 +1 9 31.733121 18.755302 20.342562 29.169015 0 +1 10 31.51068 19.338274 20.26157 28.889475 0 +1 11 31.155932 19.344704 20.729096 28.770267 0 +1 12 28.641307 21.681095 22.115748 27.561843 0.000006 +1 13 28.644403 21.190688 21.233551 28.931359 0 +1 14 27.912176 22.509522 21.398893 28.179408 0 +1 15 29.987269 20.65125 20.583967 28.777514 0 +1 16 30.695446 20.751024 19.720664 28.832866 0 +1 17 32.301494 19.466964 19.056719 29.174754 0.000069 +1 18 31.991424 19.465319 19.428886 29.114371 0 +1 19 31.223398 19.283091 20.843846 28.649665 0 +1 20 30.001159 20.431045 21.682439 27.885357 0 +1 21 30.268972 20.128608 21.518529 28.08389 0 +1 22 29.507609 20.991486 21.551678 27.949227 0 +1 23 29.228924 20.961638 22.202396 27.607042 0 +1 24 28.895271 21.140428 22.773371 27.190931 0 +1 25 30.220087 20.183506 21.007244 28.589163 0 +1 26 30.747733 19.55149 20.989765 28.711005 0.000006 +1 27 30.618992 19.162575 20.686703 29.531698 0.000031 +1 28 31.561628 19.651299 20.291748 28.495305 0.000019 +1 29 31.889741 19.244628 20.387671 28.477401 0.000559 +1 30 30.01585 20.370968 21.669604 27.943339 0.000239 +1 31 29.948939 20.187892 21.74697 28.116198 0 +1 32 29.83526 20.721207 21.226889 28.216644 0 +1 33 28.951574 21.118594 21.807089 28.122743 0 +1 34 29.250508 21.589012 20.80903 28.351444 0.000006 +1 35 29.741069 20.846087 21.339816 28.073028 0 +1 36 29.685575 20.657699 21.409349 28.247377 0 +1 37 30.435943 19.845352 21.605325 28.11328 0.0001 +1 38 31.52442 19.566381 20.859275 28.049918 0.000006 +1 39 31.915805 19.322889 20.315213 28.445698 0.000396 +1 40 31.415236 19.831291 20.60081 28.152663 0 +1 41 31.151606 20.007274 19.953602 28.887329 0.000188 +1 42 29.605015 21.700164 21.132809 27.561943 0.000069 +1 43 28.856192 21.690732 21.620633 27.832141 0.000302 +1 44 28.354815 21.89939 21.789262 27.956319 0.000214 +1 45 28.785938 21.376155 22.083299 27.443347 0.311262 +1 46 30.020967 20.974608 20.997153 28.006939 0.000333 +1 47 30.905677 19.834877 21.050285 28.209156 0.000006 +1 48 31.123254 20.025503 20.781792 28.068879 0.000572 +1 49 32.061167 19.135286 20.210972 28.592399 0.000176 +1 50 31.368968 19.831498 20.33522 28.464018 0.000295 +1 51 30.241493 20.530902 21.628272 27.599157 0.000176 +1 52 29.272115 21.228524 22.138875 27.360278 0.000208 +1 53 28.876831 20.985166 22.109191 28.028328 0.000484 +1 54 28.25128 21.263287 22.617006 27.868106 0.000321 +1 55 29.677859 20.048159 21.516525 28.756368 0.001089 +1 56 31.025964 19.638994 21.162354 28.1717 0.000988 +1 57 32.3089 19.022943 19.727314 28.939987 0.000856 +1 58 33.069967 18.780516 19.315424 28.832859 0.001234 +1 59 32.5634 19.018873 19.681712 28.735624 0.000391 +1 60 31.033388 19.63991 20.28236 29.043106 0.001235 +1 61 28.877884 21.063797 22.54864 27.508242 0.001437 +1 62 28.206236 21.933072 21.756687 28.103248 0.000757 +1 63 28.076144 21.765468 22.13245 28.025345 0.000593 +1 64 28.444021 21.930975 21.519278 28.105031 0.000694 +1 65 30.427586 20.515343 21.251214 27.804511 0.001345 +1 66 30.96119 20.454946 20.819432 27.764078 0.000354 +1 67 31.55559 19.752271 19.98091 28.7104 0.000829 +1 68 30.884355 19.787006 21.169721 28.158438 0.000481 +1 69 29.915794 19.951388 21.827419 28.302832 0.002566 +1 70 29.720163 20.878848 21.185973 28.214947 0.00007 +1 71 28.563014 21.296438 21.558676 28.580233 0.001639 +1 72 27.775812 22.725309 21.897851 27.599987 0.001041 +1 73 28.801882 22.042398 21.835818 27.319535 0.000367 +1 74 29.842933 21.375107 20.192959 28.587638 0.001363 +1 75 28.875221 21.990286 22.042923 27.09157 0 + + |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/picard_CollectRnaSeqMetrics.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/picard_CollectRnaSeqMetrics.txt Thu May 25 17:49:13 2017 -0400 |
| [ |
| @@ -0,0 +1,113 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpRJquSu/files/000/dataset_14.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpRJquSu/files/000/dataset_15.dat ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json +## htsjdk.samtools.metrics.StringHeader +# Started on: Thu Dec 08 10:55:06 CET 2016 + +## METRICS CLASS picard.analysis.RnaSeqMetrics +PF_BASES PF_ALIGNED_BASES RIBOSOMAL_BASES CODING_BASES UTR_BASES INTRONIC_BASES INTERGENIC_BASES IGNORED_READS CORRECT_STRAND_READS INCORRECT_STRAND_READS PCT_RIBOSOMAL_BASES PCT_CODING_BASES PCT_UTR_BASES PCT_INTRONIC_BASES PCT_INTERGENIC_BASES PCT_MRNA_BASES PCT_USABLE_BASES PCT_CORRECT_STRAND_READS MEDIAN_CV_COVERAGE MEDIAN_5PRIME_BIAS MEDIAN_3PRIME_BIAS MEDIAN_5PRIME_TO_3PRIME_BIAS SAMPLE LIBRARY READ_GROUP +48870 48712 0 38786 0 9926 0 0 0 0 0.796231 0 0.203769 0.796231 0.793657 0 0.91593 0.430026 0.235755 1.402829 + +## HISTOGRAM java.lang.Integer +normalized_position All_Reads.normalized_coverage +0 0.313906 +1 0.333933 +2 0.365536 +3 0.344525 +4 0.371353 +5 0.378606 +6 0.518015 +7 0.51266 +8 0.500497 +9 0.690539 +10 0.829611 +11 0.784227 +12 0.825037 +13 0.730533 +14 0.73133 +15 0.693057 +16 0.873759 +17 0.774195 +18 0.721989 +19 0.791727 +20 0.697702 +21 0.698451 +22 0.568885 +23 0.689955 +24 0.580475 +25 0.602348 +26 0.657286 +27 0.600594 +28 0.48185 +29 0.478605 +30 0.646053 +31 0.689366 +32 0.740073 +33 0.695415 +34 0.708419 +35 0.714707 +36 0.707421 +37 0.793703 +38 0.84384 +39 0.819497 +40 0.982412 +41 1.172387 +42 1.28116 +43 1.379184 +44 1.416285 +45 1.32892 +46 1.248258 +47 1.308676 +48 1.085518 +49 1.006687 +50 0.851309 +51 0.693805 +52 0.672921 +53 0.684999 +54 0.62579 +55 0.529832 +56 0.546564 +57 0.566014 +58 0.615824 +59 0.565042 +60 0.547677 +61 0.642067 +62 0.83636 +63 0.937071 +64 1.057465 +65 1.168829 +66 1.375228 +67 1.489487 +68 1.530099 +69 1.287542 +70 1.442585 +71 1.347823 +72 1.424913 +73 1.468345 +74 1.796846 +75 1.79639 +76 1.747908 +77 1.76867 +78 1.773528 +79 1.670178 +80 1.740083 +81 1.809632 +82 2.019967 +83 2.201517 +84 2.150455 +85 2.327367 +86 2.261259 +87 1.929731 +88 1.936627 +89 1.80697 +90 1.789004 +91 1.642341 +92 1.408203 +93 1.159737 +94 0.990047 +95 0.697842 +96 0.377809 +97 0.243433 +98 0.218816 +99 0.223665 +100 0.225079 + |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/report_all.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/report_all.html Thu May 25 17:49:13 2017 -0400 |
| [ |
| b'@@ -0,0 +1,5927 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+\n+ \n+\n+<meta charset="utf-8">\n+<meta http-equiv="X-UA-Compatible" content="IE=edge">\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n+<meta name="author" content="MultiQC">\n+<title>MultiQC Report</title>\n+\n+<!-- JSON plot data -->\n+<script type="text/javascript">\n+mqc_compressed_plotdata = \'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'..b'-6">\n+ <select id="tableScatter_col1" name="tableScatter_col1" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ <div class="col-sm-6">\n+ <select id="tableScatter_col2" name="tableScatter_col2" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ </div>\n+ <div class="hc-plot-wrapper">\n+ <div id="tableScatterPlot" class="hc-plot not_rendered hc-scatter-plot no-handle" style="width:566px; height: 510px;">\n+ <small>Please select two table columns.</small>\n+ </div>\n+ </div>\n+ </form>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+\n+\n+<!-- Regex Help Modal -->\n+<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n+ <div class="modal-dialog" role="document">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ <h3 class="modal-title">Regex Help</h3>\n+ </div>\n+ <div class="modal-body">\n+ <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n+ <div class="row">\n+ <div class="col-sm-6 regex_example_buttons">\n+ <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n+ <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n+ <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n+ <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n+ <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n+ <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n+ <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n+ <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n+ <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n+ <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n+ <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n+ </div>\n+ <div class="col-sm-6 regex_example_demo">\n+ <input type="text" class="form-control" />\n+<pre>\n+<span>samp_1</span>\n+<span>samp_1_edited</span>\n+<span>samp_2</span>\n+<span>samp_2_edited</span>\n+<span>samp_3</span>\n+<span>samp_3_edited</span>\n+<span>prepended_samp_1</span>\n+<span>tmp_samp_1_edited</span>\n+<span>tmpp_samp_1_edited</span>\n+<span>tmppp_samp_1_edited</span>\n+<span>#samp_1_edited.tmp</span>\n+<span>samp_11</span>\n+<span>samp_11111</span>\n+</pre>\n+ <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/report_bismark.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/report_bismark.html Thu May 25 17:49:13 2017 -0400 |
| [ |
| b'@@ -0,0 +1,4682 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+\n+ \n+\n+<meta charset="utf-8">\n+<meta http-equiv="X-UA-Compatible" content="IE=edge">\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n+<meta name="author" content="MultiQC">\n+<title>MultiQC Report</title>\n+\n+<!-- JSON plot data -->\n+<script type="text/javascript">\n+mqc_compressed_plotdata = \'N4IgRglgzgtghgJwNYH04BsIHMB2MCmOALiAFwAEoADugPZEpECeV+Z54iKWCcVAFiAA0HACZwicKPiJR2AbXmgAxrToJ2IAMQAmAGYB2fKIAcwsRLgKdOgAwBWeyYB0tgLoiQOOAU0BBTFxjcgBVHAgARwBXfHQmEABfERU1Wg0KbQAWAE4dbINbcxBxSQUARmzbTNcPDm9fDIDsHGC/GEgsKNooqDjE5JBVdU0tW1EdAGYJq08Sqwp5bIncl3dPerYMgBEIUXIAOXpyJtxEt1rB2hw9bHZQJnQ4MBHyACV8OFE5T2UqKAB3CBEZT8FCqKLEKAoR5gWKafZRdr4BDkWh6N4fL5FXaaSCwRCoDDNAjEIpEIHoTYcABC0HgyGOgTwhCI5AAyqoEPg5EkOFAfDRuQp5OA6QSUHMQOdeaL8cgUFAiLwcKI0EySSQKNQ6AxmKxcVweHxBLNLNJZMLQJKFmUyjZbAA2GrrHxUkAAeQQ2Ag3nQ5DA9CItBg5EVytE/UoxUs5VsJgm9h0zrqrs0nu9vvIQaooaVcBVZwuqmuty1gz+gOBoPBkOhTzhGQRSJRaIxn2+HHJREp/nVLKztHIAEkVRAAG67KIYci0qBRdA3Ij4dl5lUdkCKuDKJA+rCaVgIZQsoq/AFAkFgtDKcljql6DDSTwPJ6aACkbaxnhxGTx9NQYfzVUiVwDVIw3AVKTkBYRV/cVJWlBIgAA==\';\n+num_datasets_plot_limit = 50;\n+mqc_sample_names_rename = [];\n+</script>\n+\n+ \n+\n+<!-- Favicon includes -->\n+<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,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">\n+<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAGAAAABgCAYAAADimHc4AAAABGdBTUEAALGPC/xhBQAAAAFzUkdCAK7OHOkAAAA'..b'-6">\n+ <select id="tableScatter_col1" name="tableScatter_col1" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ <div class="col-sm-6">\n+ <select id="tableScatter_col2" name="tableScatter_col2" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ </div>\n+ <div class="hc-plot-wrapper">\n+ <div id="tableScatterPlot" class="hc-plot not_rendered hc-scatter-plot no-handle" style="width:566px; height: 510px;">\n+ <small>Please select two table columns.</small>\n+ </div>\n+ </div>\n+ </form>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+\n+\n+<!-- Regex Help Modal -->\n+<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n+ <div class="modal-dialog" role="document">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ <h3 class="modal-title">Regex Help</h3>\n+ </div>\n+ <div class="modal-body">\n+ <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n+ <div class="row">\n+ <div class="col-sm-6 regex_example_buttons">\n+ <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n+ <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n+ <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n+ <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n+ <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n+ <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n+ <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n+ <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n+ <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n+ <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n+ <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n+ </div>\n+ <div class="col-sm-6 regex_example_demo">\n+ <input type="text" class="form-control" />\n+<pre>\n+<span>samp_1</span>\n+<span>samp_1_edited</span>\n+<span>samp_2</span>\n+<span>samp_2_edited</span>\n+<span>samp_3</span>\n+<span>samp_3_edited</span>\n+<span>prepended_samp_1</span>\n+<span>tmp_samp_1_edited</span>\n+<span>tmpp_samp_1_edited</span>\n+<span>tmppp_samp_1_edited</span>\n+<span>#samp_1_edited.tmp</span>\n+<span>samp_11</span>\n+<span>samp_11111</span>\n+</pre>\n+ <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/report_bowtie2SE.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/report_bowtie2SE.html Thu May 25 17:49:13 2017 -0400 |
| [ |
| b'@@ -0,0 +1,4645 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+\n+ \n+\n+<meta charset="utf-8">\n+<meta http-equiv="X-UA-Compatible" content="IE=edge">\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n+<meta name="author" content="MultiQC">\n+<title>MultiQC Report</title>\n+\n+<!-- JSON plot data -->\n+<script type="text/javascript">\n+mqc_compressed_plotdata = \'N4IgRg9g7gLglgUwEwH0DOCUAcA2EYgBcABKLvijAJ5YJHHgCGATigObONYAWIANAwAmjGIwww09ANpTQAYwh5m9EAGIkABgCsANgAcAM35CRjaQEYAzEgCcNgCw7LAOg0DzGjXoDs38/dcAXQEQADtGAFs6EhAAZQBRYgiuWkFiAFdQuABHdIQcKhAAXwF5RQhlGNUDb0ZLLTljEGFRaW9LPRstbx1XAS09S297DQCNYIZwqJUEpPSceGSsVOLSkAUlFVUbPXMbPaaWsxIpevNdFzdiJGHPPSCQqeiGWdD8YkYcODZQhEFiwITdYQUIGb70UBUHCMMBbYgAJQQjEEkhC8BgOGeIAAQtB4AhrsRZgBBL4/KKhGBEhTMBCohhyLBoKBwGBybgoBSZCQoaFgfIqABy6Qi/OYxAgBgRSJRTTg/xikFgiFQGGweAIJQYaEiuDp0ik4DxKoS5iaSvxSASSBAgKKRSAAA=\';\n+num_datasets_plot_limit = 50;\n+mqc_sample_names_rename = [];\n+</script>\n+\n+ \n+\n+<!-- Favicon includes -->\n+<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,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">\n+<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAGAAAABgCAYAAADimHc4AAAABGdBTUEAALGPC/xhBQAAAAFzUkdCAK7OHOkAAAAgY0hSTQAAeiYAAICEAAD6AAAAgOgAAHUwAADqYAAAOpgAABdwnLpRPAAAAAZiS0dEAP8A/wD/oL2nkwAAAAlwSFlzAAAuIwAALiMBeKU/dgAACGNJREFUeNrtnUtsFVUYx3+37xYQ5VHlcbFURHwBPgqICBUkIXHtShcuNCZETdCFRo0LE92yMWiCCxfGLW5MatFaUBCQlJeIighSUeQRBMFSbtvr4ptpT2/vvfPNvTNzprfzS5q'..b'-6">\n+ <select id="tableScatter_col1" name="tableScatter_col1" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ <div class="col-sm-6">\n+ <select id="tableScatter_col2" name="tableScatter_col2" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ </div>\n+ <div class="hc-plot-wrapper">\n+ <div id="tableScatterPlot" class="hc-plot not_rendered hc-scatter-plot no-handle" style="width:566px; height: 510px;">\n+ <small>Please select two table columns.</small>\n+ </div>\n+ </div>\n+ </form>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+\n+\n+<!-- Regex Help Modal -->\n+<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n+ <div class="modal-dialog" role="document">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ <h3 class="modal-title">Regex Help</h3>\n+ </div>\n+ <div class="modal-body">\n+ <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n+ <div class="row">\n+ <div class="col-sm-6 regex_example_buttons">\n+ <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n+ <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n+ <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n+ <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n+ <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n+ <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n+ <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n+ <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n+ <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n+ <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n+ <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n+ </div>\n+ <div class="col-sm-6 regex_example_demo">\n+ <input type="text" class="form-control" />\n+<pre>\n+<span>samp_1</span>\n+<span>samp_1_edited</span>\n+<span>samp_2</span>\n+<span>samp_2_edited</span>\n+<span>samp_3</span>\n+<span>samp_3_edited</span>\n+<span>prepended_samp_1</span>\n+<span>tmp_samp_1_edited</span>\n+<span>tmpp_samp_1_edited</span>\n+<span>tmppp_samp_1_edited</span>\n+<span>#samp_1_edited.tmp</span>\n+<span>samp_11</span>\n+<span>samp_11111</span>\n+</pre>\n+ <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/report_cutadapt.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/report_cutadapt.html Thu May 25 17:49:13 2017 -0400 |
| [ |
| b'@@ -0,0 +1,4650 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+\n+ \n+\n+<meta charset="utf-8">\n+<meta http-equiv="X-UA-Compatible" content="IE=edge">\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n+<meta name="author" content="MultiQC">\n+<title>MultiQC Report</title>\n+\n+<!-- JSON plot data -->\n+<script type="text/javascript">\n+mqc_compressed_plotdata = \'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\';\n+num_datasets_plot_limit = 50;\n+mqc_sample_names_rename = [];\n+</script>\n+\n+ \n+\n+<!-- Favicon includes -->\n+<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,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'..b'-6">\n+ <select id="tableScatter_col1" name="tableScatter_col1" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ <div class="col-sm-6">\n+ <select id="tableScatter_col2" name="tableScatter_col2" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ </div>\n+ <div class="hc-plot-wrapper">\n+ <div id="tableScatterPlot" class="hc-plot not_rendered hc-scatter-plot no-handle" style="width:566px; height: 510px;">\n+ <small>Please select two table columns.</small>\n+ </div>\n+ </div>\n+ </form>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+\n+\n+<!-- Regex Help Modal -->\n+<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n+ <div class="modal-dialog" role="document">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ <h3 class="modal-title">Regex Help</h3>\n+ </div>\n+ <div class="modal-body">\n+ <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n+ <div class="row">\n+ <div class="col-sm-6 regex_example_buttons">\n+ <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n+ <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n+ <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n+ <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n+ <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n+ <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n+ <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n+ <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n+ <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n+ <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n+ <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n+ </div>\n+ <div class="col-sm-6 regex_example_demo">\n+ <input type="text" class="form-control" />\n+<pre>\n+<span>samp_1</span>\n+<span>samp_1_edited</span>\n+<span>samp_2</span>\n+<span>samp_2_edited</span>\n+<span>samp_3</span>\n+<span>samp_3_edited</span>\n+<span>prepended_samp_1</span>\n+<span>tmp_samp_1_edited</span>\n+<span>tmpp_samp_1_edited</span>\n+<span>tmppp_samp_1_edited</span>\n+<span>#samp_1_edited.tmp</span>\n+<span>samp_11</span>\n+<span>samp_11111</span>\n+</pre>\n+ <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/report_fastqc.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/report_fastqc.html Thu May 25 17:49:13 2017 -0400 |
| [ |
| b'@@ -0,0 +1,5477 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+\n+ \n+\n+<meta charset="utf-8">\n+<meta http-equiv="X-UA-Compatible" content="IE=edge">\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n+<meta name="author" content="MultiQC">\n+<title>MultiQC Report</title>\n+\n+<!-- JSON plot data -->\n+<script type="text/javascript">\n+mqc_compressed_plotdata = \'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'..b'-6">\n+ <select id="tableScatter_col1" name="tableScatter_col1" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ <div class="col-sm-6">\n+ <select id="tableScatter_col2" name="tableScatter_col2" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ </div>\n+ <div class="hc-plot-wrapper">\n+ <div id="tableScatterPlot" class="hc-plot not_rendered hc-scatter-plot no-handle" style="width:566px; height: 510px;">\n+ <small>Please select two table columns.</small>\n+ </div>\n+ </div>\n+ </form>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+\n+\n+<!-- Regex Help Modal -->\n+<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n+ <div class="modal-dialog" role="document">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ <h3 class="modal-title">Regex Help</h3>\n+ </div>\n+ <div class="modal-body">\n+ <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n+ <div class="row">\n+ <div class="col-sm-6 regex_example_buttons">\n+ <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n+ <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n+ <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n+ <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n+ <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n+ <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n+ <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n+ <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n+ <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n+ <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n+ <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n+ </div>\n+ <div class="col-sm-6 regex_example_demo">\n+ <input type="text" class="form-control" />\n+<pre>\n+<span>samp_1</span>\n+<span>samp_1_edited</span>\n+<span>samp_2</span>\n+<span>samp_2_edited</span>\n+<span>samp_3</span>\n+<span>samp_3_edited</span>\n+<span>prepended_samp_1</span>\n+<span>tmp_samp_1_edited</span>\n+<span>tmpp_samp_1_edited</span>\n+<span>tmppp_samp_1_edited</span>\n+<span>#samp_1_edited.tmp</span>\n+<span>samp_11</span>\n+<span>samp_11111</span>\n+</pre>\n+ <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/report_fastqc_2.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/report_fastqc_2.html Thu May 25 17:49:13 2017 -0400 |
| [ |
| b'@@ -0,0 +1,5477 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+\n+ \n+\n+<meta charset="utf-8">\n+<meta http-equiv="X-UA-Compatible" content="IE=edge">\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n+<meta name="author" content="MultiQC">\n+<title>MultiQC Report</title>\n+\n+<!-- JSON plot data -->\n+<script type="text/javascript">\n+mqc_compressed_plotdata = \'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'..b'-6">\n+ <select id="tableScatter_col1" name="tableScatter_col1" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ <div class="col-sm-6">\n+ <select id="tableScatter_col2" name="tableScatter_col2" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ </div>\n+ <div class="hc-plot-wrapper">\n+ <div id="tableScatterPlot" class="hc-plot not_rendered hc-scatter-plot no-handle" style="width:566px; height: 510px;">\n+ <small>Please select two table columns.</small>\n+ </div>\n+ </div>\n+ </form>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+\n+\n+<!-- Regex Help Modal -->\n+<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n+ <div class="modal-dialog" role="document">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ <h3 class="modal-title">Regex Help</h3>\n+ </div>\n+ <div class="modal-body">\n+ <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n+ <div class="row">\n+ <div class="col-sm-6 regex_example_buttons">\n+ <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n+ <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n+ <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n+ <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n+ <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n+ <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n+ <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n+ <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n+ <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n+ <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n+ <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n+ </div>\n+ <div class="col-sm-6 regex_example_demo">\n+ <input type="text" class="form-control" />\n+<pre>\n+<span>samp_1</span>\n+<span>samp_1_edited</span>\n+<span>samp_2</span>\n+<span>samp_2_edited</span>\n+<span>samp_3</span>\n+<span>samp_3_edited</span>\n+<span>prepended_samp_1</span>\n+<span>tmp_samp_1_edited</span>\n+<span>tmpp_samp_1_edited</span>\n+<span>tmppp_samp_1_edited</span>\n+<span>#samp_1_edited.tmp</span>\n+<span>samp_11</span>\n+<span>samp_11111</span>\n+</pre>\n+ <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/report_featurecounts.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/report_featurecounts.html Thu May 25 17:49:13 2017 -0400 |
| [ |
| b'@@ -0,0 +1,4656 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+\n+ \n+\n+<meta charset="utf-8">\n+<meta http-equiv="X-UA-Compatible" content="IE=edge">\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n+<meta name="author" content="MultiQC">\n+<title>MultiQC Report</title>\n+\n+<!-- JSON plot data -->\n+<script type="text/javascript">\n+mqc_compressed_plotdata = \'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\';\n+num_datasets_plot_limit = 50;\n+mqc_sample_names_rename = [];\n+</script>\n+\n+ \n+\n+<!-- Favicon includes -->\n+<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACAAAAAgCAMAAABEpIrGAAAABGdBTUEAALGPC/xhBQAAAAFzUkdCAK7OHOkAAAAgY0hSTQAAeiYAAICEAAD6AAAAgOgAAHUwAADqYAAAOpgAABdwnLpRPAAAAgRQTFRFAAAAHR0bvhYi0QkfuRojAJZAAJY/IWzIHnC9HXG4HR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bvhYivhYivhYivhYivhYivhYivhYiwBUiwRQhwRQhwxIh3gEdyBAgQGs2KHs6KXo6KXo5JX06BZI/AJhAAJdAAJdAAJc/AJc+AJc+AJc+AJc8AJ0pBo9XFHyUFnqbFnqaGXemHXG5H2/AHXG5HXG5HXG5HXG4HXG4HXG4HXG4HXG4HXG4HXG4HR0b////FByqhAAAAKp0Uk5TAAAAAAAAAAAAAAESGBcRBgoJnNPQ0rQcWVoLwPtXAqFuv5Mk3NoibP79XQSo+vSbAyzj9+7H4Cl18s7wifFjB7C9nryjBTTpdJFQgOYvfe04Nexot6yXYrKrPeo2heIromkq4ZlrpbFRtW1k/MjUHbuY9ktSw8R673h3M2ETOj08FhiRvLi6aAIJMEtKSkkzBzyxurm6sTkBEj1JSUEeAmq9vL6UHQcWFwlLDobJAAAAAWJLR0SryQFnKAAAAAlwSFlzAAAuIwAALiMBeKU/dgAAAa5JREFUOMut0tdXE0EYBfD9QBRIIgkEDZDQhUBQAgGlBCIlSlGqSlFBVKoiSu8oHQWpIhaUpuD9K50JOXlgJm/cp2/u+Z3dnZ1RFApUqTUa9eVAUk5DQRoWtdaz1gWH6PWhV656CoOeJTTMsw6PAIvR5C4oMoqvEe0B2hhXEet+B8XFy8G1BDdINMtBUrKrIUsKJOD6DSDVyitKS4fZZj4LMjKBm7dcIAvIzhGekGvPgzmfVeS4DRQUCsBmKgKKnaTQnbtASakAjGXlwL37RFQBVFbFCiDJUF0D1BJpHwAPHY/EbdZZ6oEGBzVmcJcqglr+9Y+f0FOgqZmeiaCFnr9gZTibX1qtDSJoJWsb0N6RDaOBHJ0i6CJ69RqV3cCbHtK9lYKeEID9YjuRrkgK6B0/o94+b0ChfhsbBlTegWqQDUMkANeV44DswHAjG84Ap2FkdHSMn2Rz1sg4u8xkMbmb88nE5JSXvP/g48PA9MzsnDzzC4u+DFxY+vhpWZqVz6trfkz4rW9sbknzZfvrRQ52vn3/Ic/P3V+XmPD/vbd/IM/h0R++kYC/x95y8u8/kOgi2/X4mGIAAAAldEVYdGRhdGU6Y3JlYXRlADIwMTYtMDQtMTlUMDk6MjM6NDErMDA6MDCtzsBUAAAAJXRFWHRkYXRlOm1vZGlmeQAyMDE2LTA0LTE5VDA5OjIzOjQxKzAwOjAw3JN46AAAAEZ0RVh0c29mdHdhcmUASW1hZ2VNYWdpY2sgNi43LjgtOSAyMDE0LTA1LTEyIFExNiBodHRwOi8vd3d3LmltYWdlbWFnaWNrLm9yZ9yG7QAAAAAYdEVYdFRodW1iOjpEb2N1bWVudDo6UGFnZXMAMaf/uy8AAAAYdEVYdFRodW1iOjpJbWFnZTo6aGVpZ2h0ADE5Mg8AcoUAAAAXdEVYdFRodW1iOjpJbWFnZTo6V2lkdGgAMTky06whCAAAABl0RVh0VGh1bWI6Ok1pbWV0eXBlAGltYWdlL3BuZz+yVk4AAAAXdEVYdFRodW1iOjpNVGltZQAxNDYxMDU3ODIxUvThswAAAA90RVh0VGh1bWI6OlNpemUAMEJClKI+7AAAAFZ0RVh0VGh1bWI6OlVSSQBmaWxlOi8vL21udGxvZy9mYXZpY29ucy8yMDE2LTA0LTE5L2Y2MDUzNWMzMThlMzdlYmRhNzJkZTJlNTJhNWJiNzk5Lmljby5wbme1EtGEAAAAAElFTkSuQmCC">\n+<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAGA'..b'-6">\n+ <select id="tableScatter_col1" name="tableScatter_col1" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ <div class="col-sm-6">\n+ <select id="tableScatter_col2" name="tableScatter_col2" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ </div>\n+ <div class="hc-plot-wrapper">\n+ <div id="tableScatterPlot" class="hc-plot not_rendered hc-scatter-plot no-handle" style="width:566px; height: 510px;">\n+ <small>Please select two table columns.</small>\n+ </div>\n+ </div>\n+ </form>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+\n+\n+<!-- Regex Help Modal -->\n+<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n+ <div class="modal-dialog" role="document">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ <h3 class="modal-title">Regex Help</h3>\n+ </div>\n+ <div class="modal-body">\n+ <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n+ <div class="row">\n+ <div class="col-sm-6 regex_example_buttons">\n+ <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n+ <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n+ <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n+ <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n+ <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n+ <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n+ <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n+ <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n+ <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n+ <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n+ <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n+ </div>\n+ <div class="col-sm-6 regex_example_demo">\n+ <input type="text" class="form-control" />\n+<pre>\n+<span>samp_1</span>\n+<span>samp_1_edited</span>\n+<span>samp_2</span>\n+<span>samp_2_edited</span>\n+<span>samp_3</span>\n+<span>samp_3_edited</span>\n+<span>prepended_samp_1</span>\n+<span>tmp_samp_1_edited</span>\n+<span>tmpp_samp_1_edited</span>\n+<span>tmppp_samp_1_edited</span>\n+<span>#samp_1_edited.tmp</span>\n+<span>samp_11</span>\n+<span>samp_11111</span>\n+</pre>\n+ <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/report_htseq.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/report_htseq.html Thu May 25 17:49:13 2017 -0400 |
| [ |
| b'@@ -0,0 +1,4656 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+\n+ \n+\n+<meta charset="utf-8">\n+<meta http-equiv="X-UA-Compatible" content="IE=edge">\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n+<meta name="author" content="MultiQC">\n+<title>MultiQC Report</title>\n+\n+<!-- JSON plot data -->\n+<script type="text/javascript">\n+mqc_compressed_plotdata = \'N4IgFgLgzgpgjgfQIZSgSwOYDsC2MsQIAOANgPYQgBcABKKRQhAJ5EzU0gBGSATghl5IiYEABpOAEyQQUMaBwDai0NNlKADADoNAXQkgsSPBxABBVJiwxJIAL4TVMpJp37ORk7XM4umAK5k/lD2jiBqLrSK2noGnuzeZiRWeAQ0AHIUNACqWGhw/uwOdOHOSgCMAJxuccYJnJk0AGIwMv68RWERrrEedaYAKmRkNAAyZADuNEgAiv5IJKEl3VHlAMxrAGw1fV4NWUlWNva67iAAxmRYAGaYHKDMJEhcpgDENABKrZIhBmBokhgCAAXjBeGQEOcZCFaNcFrADOciFAJmgIOcwJCggQoAgnlwYItvOl/L4wTQyNdPt9fpwAaZILBECh0NhUoQGJQDBA0SR6iAABIDADK8BoAGFsRAaBZWbh8ApiiAoMZSDAYTRlOBoPAEN1TnY7EAAAA==\';\n+num_datasets_plot_limit = 50;\n+mqc_sample_names_rename = [];\n+</script>\n+\n+ \n+\n+<!-- Favicon includes -->\n+<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,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">\n+<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAGAAAABgCAYAAADimHc4AAAABGdBTUEAALGPC/xhBQAAAAFzUkdCAK7OHOkAAAAgY0hSTQAAeiYAAICEAAD6AAAAgOgAAHUwAADqYAAAOpgAABdwnLpRPAAAAAZiS0dEAP8A/wD/oL2nkwAAAAlwSFlzAAAuIwAALiMBeKU/dgAACGNJREFUeNrtnUtsFVUYx3+37xYQ5VHlcbFURHwBPgqICBUkIXHtShcuNCZETdCFRo0LE92yMWiCCxfGLW5MatFaUBCQlJeIighSUeQRBMFSbtvr4ptpT2/vvfPNvTNzprfzS5q0tzPnzJn/fN85833nnAs'..b'-6">\n+ <select id="tableScatter_col1" name="tableScatter_col1" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ <div class="col-sm-6">\n+ <select id="tableScatter_col2" name="tableScatter_col2" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ </div>\n+ <div class="hc-plot-wrapper">\n+ <div id="tableScatterPlot" class="hc-plot not_rendered hc-scatter-plot no-handle" style="width:566px; height: 510px;">\n+ <small>Please select two table columns.</small>\n+ </div>\n+ </div>\n+ </form>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+\n+\n+<!-- Regex Help Modal -->\n+<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n+ <div class="modal-dialog" role="document">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ <h3 class="modal-title">Regex Help</h3>\n+ </div>\n+ <div class="modal-body">\n+ <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n+ <div class="row">\n+ <div class="col-sm-6 regex_example_buttons">\n+ <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n+ <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n+ <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n+ <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n+ <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n+ <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n+ <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n+ <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n+ <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n+ <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n+ <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n+ </div>\n+ <div class="col-sm-6 regex_example_demo">\n+ <input type="text" class="form-control" />\n+<pre>\n+<span>samp_1</span>\n+<span>samp_1_edited</span>\n+<span>samp_2</span>\n+<span>samp_2_edited</span>\n+<span>samp_3</span>\n+<span>samp_3_edited</span>\n+<span>prepended_samp_1</span>\n+<span>tmp_samp_1_edited</span>\n+<span>tmpp_samp_1_edited</span>\n+<span>tmppp_samp_1_edited</span>\n+<span>#samp_1_edited.tmp</span>\n+<span>samp_11</span>\n+<span>samp_11111</span>\n+</pre>\n+ <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/report_picard.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/report_picard.html Thu May 25 17:49:13 2017 -0400 |
| [ |
| b'@@ -0,0 +1,4826 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+\n+ \n+\n+<meta charset="utf-8">\n+<meta http-equiv="X-UA-Compatible" content="IE=edge">\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n+<meta name="author" content="MultiQC">\n+<title>MultiQC Report</title>\n+\n+<!-- JSON plot data -->\n+<script type="text/javascript">\n+mqc_compressed_plotdata = \'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'..b'-6">\n+ <select id="tableScatter_col1" name="tableScatter_col1" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ <div class="col-sm-6">\n+ <select id="tableScatter_col2" name="tableScatter_col2" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ </div>\n+ <div class="hc-plot-wrapper">\n+ <div id="tableScatterPlot" class="hc-plot not_rendered hc-scatter-plot no-handle" style="width:566px; height: 510px;">\n+ <small>Please select two table columns.</small>\n+ </div>\n+ </div>\n+ </form>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+\n+\n+<!-- Regex Help Modal -->\n+<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n+ <div class="modal-dialog" role="document">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ <h3 class="modal-title">Regex Help</h3>\n+ </div>\n+ <div class="modal-body">\n+ <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n+ <div class="row">\n+ <div class="col-sm-6 regex_example_buttons">\n+ <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n+ <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n+ <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n+ <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n+ <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n+ <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n+ <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n+ <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n+ <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n+ <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n+ <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n+ </div>\n+ <div class="col-sm-6 regex_example_demo">\n+ <input type="text" class="form-control" />\n+<pre>\n+<span>samp_1</span>\n+<span>samp_1_edited</span>\n+<span>samp_2</span>\n+<span>samp_2_edited</span>\n+<span>samp_3</span>\n+<span>samp_3_edited</span>\n+<span>prepended_samp_1</span>\n+<span>tmp_samp_1_edited</span>\n+<span>tmpp_samp_1_edited</span>\n+<span>tmppp_samp_1_edited</span>\n+<span>#samp_1_edited.tmp</span>\n+<span>samp_11</span>\n+<span>samp_11111</span>\n+</pre>\n+ <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/report_rnastar_counts.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/report_rnastar_counts.html Thu May 25 17:49:13 2017 -0400 |
| [ |
| b'@@ -0,0 +1,4586 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+\n+ \n+\n+<meta charset="utf-8">\n+<meta http-equiv="X-UA-Compatible" content="IE=edge">\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n+<meta name="author" content="MultiQC">\n+<title>MultiQC Report</title>\n+\n+<!-- JSON plot data -->\n+<script type="text/javascript">\n+mqc_compressed_plotdata = \'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\';\n+num_datasets_plot_limit = 50;\n+mqc_sample_names_rename = [];\n+</script>\n+\n+ \n+\n+<!-- Favicon includes -->\n+<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,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">\n+<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAGAAAABgCAYAAADimHc4AAAABGdBTUEAALGPC/xhBQAAAAFzUkdCAK7OHOkAAAAgY0hSTQAAeiYAAICEAAD6AAAAgOgAAHUwAADqYAAAOpgAABdwnLpRPAAAAAZiS0dEAP8A/wD/oL2nkwAAAAlwSFlzAAAuIwA'..b'-6">\n+ <select id="tableScatter_col1" name="tableScatter_col1" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ <div class="col-sm-6">\n+ <select id="tableScatter_col2" name="tableScatter_col2" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ </div>\n+ <div class="hc-plot-wrapper">\n+ <div id="tableScatterPlot" class="hc-plot not_rendered hc-scatter-plot no-handle" style="width:566px; height: 510px;">\n+ <small>Please select two table columns.</small>\n+ </div>\n+ </div>\n+ </form>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+\n+\n+<!-- Regex Help Modal -->\n+<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n+ <div class="modal-dialog" role="document">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ <h3 class="modal-title">Regex Help</h3>\n+ </div>\n+ <div class="modal-body">\n+ <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n+ <div class="row">\n+ <div class="col-sm-6 regex_example_buttons">\n+ <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n+ <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n+ <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n+ <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n+ <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n+ <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n+ <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n+ <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n+ <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n+ <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n+ <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n+ </div>\n+ <div class="col-sm-6 regex_example_demo">\n+ <input type="text" class="form-control" />\n+<pre>\n+<span>samp_1</span>\n+<span>samp_1_edited</span>\n+<span>samp_2</span>\n+<span>samp_2_edited</span>\n+<span>samp_3</span>\n+<span>samp_3_edited</span>\n+<span>prepended_samp_1</span>\n+<span>tmp_samp_1_edited</span>\n+<span>tmpp_samp_1_edited</span>\n+<span>tmppp_samp_1_edited</span>\n+<span>#samp_1_edited.tmp</span>\n+<span>samp_11</span>\n+<span>samp_11111</span>\n+</pre>\n+ <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/report_rnastar_log.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/report_rnastar_log.html Thu May 25 17:49:13 2017 -0400 |
| [ |
| b'@@ -0,0 +1,4658 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+\n+ \n+\n+<meta charset="utf-8">\n+<meta http-equiv="X-UA-Compatible" content="IE=edge">\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n+<meta name="author" content="MultiQC">\n+<title>MultiQC Report</title>\n+\n+<!-- JSON plot data -->\n+<script type="text/javascript">\n+mqc_compressed_plotdata = \'N4IgzgLghgTg+lANgSwOYDsC2BTdE4AOiA9hCAFwAEoRpcEAngdhZSAEaxyoxQEAWIADRsAJlGhhsEMKwDac0AGNiJGKxABiACwBmAOzt2ARmFiJUeQA4AnADoADAF0RIdFBwaAqumQBHAFdsRAZKTD5mURAAXxFlVWJ1Ki19JXYAVmwlMxBxaHljRxc2d09kgFkI7FFKCGIwgMQIZCJsShIlZBi4kBU1DU0TByttbNc8yyo5Ywci11KWZJ9wgkiqOvqwfkSyaKdi3uJ0ADM0VlAGRCh2AcoAJWwoUVlXJQIwAHdkCCV+OBUAngwHAruxghoAHIBTBgmCUYjHe6PZ45ZBRZKQLhINBYXD4WhkVzNCCIRZsADKABUAIJ3SjUlAYHB4SjklQwbCyWJsMAeVqyKZyEAwdyY+AkVAgfbRaJAAA==\';\n+num_datasets_plot_limit = 50;\n+mqc_sample_names_rename = [];\n+</script>\n+\n+ \n+\n+<!-- Favicon includes -->\n+<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,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">\n+<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAGAAAABgCAYAAADimHc4AAAABGdBTUEAALGPC/xhBQAAAAFzUkdCAK7OHOkAAAAgY0hSTQAAeiYAAICEAAD6AAAAgOgAAHUwAADqYAAAOpgAABdwnLpRPAAAAAZiS0dEAP8A/wD/oL2nkwAAAAlwSFlzAAAuIwAALiMBeKU/dgAACGNJREFUeNrtnUtsFVUYx3+37xYQ5VHlcbFURHwBPgqICBUkIXHtShcuNCZETdCFRo0LE92yMWiCCxfGLW5MatFaUBCQlJeIighSUeQRBMFSbtvr4ptpT2/vvfPNvTNzprfzS5q0tzPnzJn/fN85833nnAsJCROZVLF/ptNz3F/rgboy67oOZHp7z0T'..b'-6">\n+ <select id="tableScatter_col1" name="tableScatter_col1" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ <div class="col-sm-6">\n+ <select id="tableScatter_col2" name="tableScatter_col2" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ </div>\n+ <div class="hc-plot-wrapper">\n+ <div id="tableScatterPlot" class="hc-plot not_rendered hc-scatter-plot no-handle" style="width:566px; height: 510px;">\n+ <small>Please select two table columns.</small>\n+ </div>\n+ </div>\n+ </form>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+\n+\n+<!-- Regex Help Modal -->\n+<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n+ <div class="modal-dialog" role="document">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ <h3 class="modal-title">Regex Help</h3>\n+ </div>\n+ <div class="modal-body">\n+ <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n+ <div class="row">\n+ <div class="col-sm-6 regex_example_buttons">\n+ <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n+ <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n+ <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n+ <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n+ <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n+ <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n+ <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n+ <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n+ <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n+ <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n+ <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n+ </div>\n+ <div class="col-sm-6 regex_example_demo">\n+ <input type="text" class="form-control" />\n+<pre>\n+<span>samp_1</span>\n+<span>samp_1_edited</span>\n+<span>samp_2</span>\n+<span>samp_2_edited</span>\n+<span>samp_3</span>\n+<span>samp_3_edited</span>\n+<span>prepended_samp_1</span>\n+<span>tmp_samp_1_edited</span>\n+<span>tmpp_samp_1_edited</span>\n+<span>tmppp_samp_1_edited</span>\n+<span>#samp_1_edited.tmp</span>\n+<span>samp_11</span>\n+<span>samp_11111</span>\n+</pre>\n+ <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/report_samtools.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/report_samtools.html Thu May 25 17:49:13 2017 -0400 |
| [ |
| b'@@ -0,0 +1,4747 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+\n+ \n+\n+<meta charset="utf-8">\n+<meta http-equiv="X-UA-Compatible" content="IE=edge">\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n+<meta name="author" content="MultiQC">\n+<title>MultiQC Report</title>\n+\n+<!-- JSON plot data -->\n+<script type="text/javascript">\n+mqc_compressed_plotdata = \'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\';\n+num_datasets_plot_limit = 50;\n+mqc_sample_names_rename = [];\n+</script>\n+\n+ \n+\n+<!-- Favicon includes -->\n+<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACAAAAAgCAMAAABEpIrGAAAABGdBTUEAALGPC/xhBQAAAAFzUkdCAK7OHOkAAAAgY0hSTQAAeiYAAICEAAD6AAAAgOgAAHUwAADqYAAAOpgAABdwnLpRPAAAAgRQTFRFAAAAHR0bvhYi0QkfuRojAJZAAJY/IWzIHnC9HXG4HR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0'..b'-6">\n+ <select id="tableScatter_col1" name="tableScatter_col1" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ <div class="col-sm-6">\n+ <select id="tableScatter_col2" name="tableScatter_col2" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ </div>\n+ <div class="hc-plot-wrapper">\n+ <div id="tableScatterPlot" class="hc-plot not_rendered hc-scatter-plot no-handle" style="width:566px; height: 510px;">\n+ <small>Please select two table columns.</small>\n+ </div>\n+ </div>\n+ </form>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+\n+\n+<!-- Regex Help Modal -->\n+<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n+ <div class="modal-dialog" role="document">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ <h3 class="modal-title">Regex Help</h3>\n+ </div>\n+ <div class="modal-body">\n+ <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n+ <div class="row">\n+ <div class="col-sm-6 regex_example_buttons">\n+ <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n+ <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n+ <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n+ <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n+ <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n+ <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n+ <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n+ <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n+ <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n+ <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n+ <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n+ </div>\n+ <div class="col-sm-6 regex_example_demo">\n+ <input type="text" class="form-control" />\n+<pre>\n+<span>samp_1</span>\n+<span>samp_1_edited</span>\n+<span>samp_2</span>\n+<span>samp_2_edited</span>\n+<span>samp_3</span>\n+<span>samp_3_edited</span>\n+<span>prepended_samp_1</span>\n+<span>tmp_samp_1_edited</span>\n+<span>tmpp_samp_1_edited</span>\n+<span>tmppp_samp_1_edited</span>\n+<span>#samp_1_edited.tmp</span>\n+<span>samp_11</span>\n+<span>samp_11111</span>\n+</pre>\n+ <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/report_samtools_idxstats.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/report_samtools_idxstats.html Thu May 25 17:49:13 2017 -0400 |
| [ |
| b'@@ -0,0 +1,4605 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+\n+ \n+\n+<meta charset="utf-8">\n+<meta http-equiv="X-UA-Compatible" content="IE=edge">\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n+<meta name="author" content="MultiQC">\n+<title>MultiQC Report</title>\n+\n+<!-- JSON plot data -->\n+<script type="text/javascript">\n+mqc_compressed_plotdata = \'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\';\n+num_datasets_plot_limit = 50;\n+mqc_sample_names_rename = [];\n+</script>\n+\n+ \n+\n+<!-- Favicon includes -->\n+<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,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'..b'-6">\n+ <select id="tableScatter_col1" name="tableScatter_col1" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ <div class="col-sm-6">\n+ <select id="tableScatter_col2" name="tableScatter_col2" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ </div>\n+ <div class="hc-plot-wrapper">\n+ <div id="tableScatterPlot" class="hc-plot not_rendered hc-scatter-plot no-handle" style="width:566px; height: 510px;">\n+ <small>Please select two table columns.</small>\n+ </div>\n+ </div>\n+ </form>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+\n+\n+<!-- Regex Help Modal -->\n+<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n+ <div class="modal-dialog" role="document">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ <h3 class="modal-title">Regex Help</h3>\n+ </div>\n+ <div class="modal-body">\n+ <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n+ <div class="row">\n+ <div class="col-sm-6 regex_example_buttons">\n+ <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n+ <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n+ <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n+ <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n+ <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n+ <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n+ <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n+ <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n+ <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n+ <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n+ <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n+ </div>\n+ <div class="col-sm-6 regex_example_demo">\n+ <input type="text" class="form-control" />\n+<pre>\n+<span>samp_1</span>\n+<span>samp_1_edited</span>\n+<span>samp_2</span>\n+<span>samp_2_edited</span>\n+<span>samp_3</span>\n+<span>samp_3_edited</span>\n+<span>prepended_samp_1</span>\n+<span>tmp_samp_1_edited</span>\n+<span>tmpp_samp_1_edited</span>\n+<span>tmppp_samp_1_edited</span>\n+<span>#samp_1_edited.tmp</span>\n+<span>samp_11</span>\n+<span>samp_11111</span>\n+</pre>\n+ <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/report_tophat.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/report_tophat.html Thu May 25 17:49:13 2017 -0400 |
| [ |
| b'@@ -0,0 +1,4656 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+\n+ \n+\n+<meta charset="utf-8">\n+<meta http-equiv="X-UA-Compatible" content="IE=edge">\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n+<meta name="author" content="MultiQC">\n+<title>MultiQC Report</title>\n+\n+<!-- JSON plot data -->\n+<script type="text/javascript">\n+mqc_compressed_plotdata = \'N4IgLg9gDgFghmA+nANgSwOYDsC2BTLMEALgAJQoUIkwBPKPE0kAIzgCdEN25YQAaZgBMEcAM54wYpgG0ZoAMYQq7JiADEAFgDMAdhYsAjAOGjZ2gAy7d27QDoLAXUEgscfGoCC6bHiEgAX0FFZQhVMg0AM104bQBWBRMQETA4WTiANm0ADgdnZjcPCIBZAFcUMDQcXgZ/IPIQJRU1dTwszQBOYxcUtLIZbU08l0LGCIARNDEldhFCUmqoKDQsDGl6kOaI9V1Ii32LJN7ZACYO7Ljhgvcx5gA5alJUTCw/QMd8xogsSMwmUFoKDgLBapAASng4EJpC4FFAxAB3NBgBQwRBKUqEMSIIEsPAoNR3Uo4PHsUgQSLgyHQpJofwRSCwBDIHy4AhEFyVMAoW4gAAq0HgYFI3he+HmAGUZnh1i4xO5KDLZDJwILmccPgEAkAAA=\';\n+num_datasets_plot_limit = 50;\n+mqc_sample_names_rename = [];\n+</script>\n+\n+ \n+\n+<!-- Favicon includes -->\n+<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,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">\n+<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAGAAAABgCAYAAADimHc4AAAABGdBTUEAALGPC/xhBQAAAAFzUkdCAK7OHOkAAAAgY0hSTQAAeiYAAICEAAD6AAAAgOgAAHUwAADqYAAAOpgAABdwnLpRPAAAAAZiS0dEAP8A/wD/oL2nkwAAAAlwSFlzAAAuIwAALiMBeKU/dgAACGNJREFUeNrtnUtsFVUYx3+37xYQ5VHlcbFURHwBPgqICBUkIXHtShcuNCZETdCFRo0LE92yMWiCCxfGLW5MatFaUBCQlJeIighSUeQRBMFSbtvr4ptpT2/vvfPNvTNzprfzS5q0tzPnzJn/fN85833nnAsJCROZVLF/ptN'..b'-6">\n+ <select id="tableScatter_col1" name="tableScatter_col1" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ <div class="col-sm-6">\n+ <select id="tableScatter_col2" name="tableScatter_col2" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ </div>\n+ <div class="hc-plot-wrapper">\n+ <div id="tableScatterPlot" class="hc-plot not_rendered hc-scatter-plot no-handle" style="width:566px; height: 510px;">\n+ <small>Please select two table columns.</small>\n+ </div>\n+ </div>\n+ </form>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+\n+\n+<!-- Regex Help Modal -->\n+<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n+ <div class="modal-dialog" role="document">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ <h3 class="modal-title">Regex Help</h3>\n+ </div>\n+ <div class="modal-body">\n+ <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n+ <div class="row">\n+ <div class="col-sm-6 regex_example_buttons">\n+ <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n+ <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n+ <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n+ <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n+ <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n+ <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n+ <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n+ <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n+ <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n+ <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n+ <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n+ </div>\n+ <div class="col-sm-6 regex_example_demo">\n+ <input type="text" class="form-control" />\n+<pre>\n+<span>samp_1</span>\n+<span>samp_1_edited</span>\n+<span>samp_2</span>\n+<span>samp_2_edited</span>\n+<span>samp_3</span>\n+<span>samp_3_edited</span>\n+<span>prepended_samp_1</span>\n+<span>tmp_samp_1_edited</span>\n+<span>tmpp_samp_1_edited</span>\n+<span>tmppp_samp_1_edited</span>\n+<span>#samp_1_edited.tmp</span>\n+<span>samp_11</span>\n+<span>samp_11111</span>\n+</pre>\n+ <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/rnastar_counts.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/rnastar_counts.txt Thu May 25 17:49:13 2017 -0400 |
| b |
| @@ -0,0 +1,5 @@ +N_unmapped 0 0 0 +N_multimapping 1 1 1 +N_noFeature 0 51 48 +N_ambiguous 0 0 0 +GENE1 99 48 51 |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/rnastar_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/rnastar_log.txt Thu May 25 17:49:13 2017 -0400 |
| b |
| @@ -0,0 +1,34 @@ + Started job on | Mar 01 15:53:05 + Started mapping on | Mar 01 15:53:08 + Finished on | Mar 01 15:53:08 + Mapping speed, Million of reads per hour | inf + + Number of input reads | 100 + Average input read length | 75 + UNIQUE READS: + Uniquely mapped reads number | 89 + Uniquely mapped reads % | 89.00% + Average mapped length | 74.80 + Number of splices: Total | 47 + Number of splices: Annotated (sjdb) | 0 + Number of splices: GT/AG | 47 + Number of splices: GC/AG | 0 + Number of splices: AT/AC | 0 + Number of splices: Non-canonical | 0 + Mismatch rate per base, % | 1.73% + Deletion rate per base | 0.00% + Deletion average length | 0.00 + Insertion rate per base | 0.00% + Insertion average length | 0.00 + MULTI-MAPPING READS: + Number of reads mapped to multiple loci | 1 + % of reads mapped to multiple loci | 1.00% + Number of reads mapped to too many loci | 0 + % of reads mapped to too many loci | 0.00% + UNMAPPED READS: + % of reads unmapped: too many mismatches | 0.00% + % of reads unmapped: too short | 10.00% + % of reads unmapped: other | 0.00% + CHIMERIC READS: + Number of chimeric reads | 0 + % of chimeric reads | 0.00% |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/samtools_flagstat.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/samtools_flagstat.txt Thu May 25 17:49:13 2017 -0400 |
| b |
| @@ -0,0 +1,13 @@ +21040602 + 0 in total (QC-passed reads + QC-failed reads) +0 + 0 secondary +0 + 0 supplementary +5448463 + 0 duplicates +20689039 + 0 mapped (98.33%:-nan%) +0 + 0 paired in sequencing +0 + 0 read1 +0 + 0 read2 +0 + 0 properly paired (-nan%:-nan%) +0 + 0 with itself and mate mapped +0 + 0 singletons (-nan%:-nan%) +0 + 0 with mate mapped to a different chr +0 + 0 with mate mapped to a different chr (mapQ>=5) |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/samtools_idxstats.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/samtools_idxstats.txt Thu May 25 17:49:13 2017 -0400 |
| b |
| @@ -0,0 +1,67 @@ +1 195471971 977171 0 +10 130694993 637405 0 +11 122082543 557954 0 +12 120129022 822778 0 +13 120421639 595176 0 +14 124902244 1179793 0 +15 104043685 474303 0 +16 98207768 450478 0 +17 94987271 442543 0 +18 90702639 423431 0 +19 61431566 269193 0 +2 182113224 2369317 0 +3 160039680 802543 0 +4 156508116 738160 0 +5 151834684 703632 0 +6 149736546 768256 0 +7 145441459 685296 0 +8 129401213 895718 0 +9 124595110 1144967 0 +MT 16299 141 0 +X 171031299 506800 0 +Y 91744698 132190 0 +JH584299.1 953012 2185 0 +GL456233.1 336933 1053 0 +JH584301.1 259875 303 0 +GL456211.1 241735 2348 0 +GL456350.1 227966 283 0 +JH584293.1 207968 236 0 +GL456221.1 206961 2196 0 +JH584297.1 205776 366 0 +JH584296.1 199368 368 0 +GL456354.1 195993 591 0 +JH584294.1 191905 313 0 +JH584298.1 184189 277 0 +JH584300.1 182347 230 0 +GL456219.1 175968 622 0 +GL456210.1 169725 1661 0 +JH584303.1 158099 214 0 +JH584302.1 155838 185 0 +GL456212.1 153618 1979 0 +JH584304.1 114452 278844 0 +GL456379.1 72385 210 0 +GL456216.1 66673 341 0 +GL456393.1 55711 629 0 +GL456366.1 47073 244 0 +GL456367.1 42057 245 0 +GL456239.1 40056 214 0 +GL456213.1 39340 99 0 +GL456383.1 38659 848 0 +GL456385.1 35240 155 0 +GL456360.1 31704 165 0 +GL456378.1 31602 444 0 +GL456389.1 28772 6166 0 +GL456372.1 28664 211 0 +GL456370.1 26764 502 0 +GL456381.1 25871 55 0 +GL456387.1 24685 156 0 +GL456390.1 24668 780 0 +GL456394.1 24323 114 0 +GL456392.1 23629 21116 0 +GL456382.1 23158 57 0 +GL456359.1 22974 85 0 +GL456396.1 21240 20375 0 +GL456368.1 20208 319 0 +JH584292.1 14945 85 0 +JH584295.1 1976 4 0 +* 0 0 274008 |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/samtools_stats.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/samtools_stats.txt Thu May 25 17:49:13 2017 -0400 |
| [ |
| b'@@ -0,0 +1,9736 @@\n+# This file was produced by samtools stats (1.2+htslib-1.2.1) and can be plotted using plot-bamstats\n+# The command line was: stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /omaha-beach/cloud_26/files/000/dataset_20.dat /omaha-beach/cloud_26/files/000/dataset_114.dat\n+# CHK, Checksum\t[2]Read Names\t[3]Sequences\t[4]Qualities\n+# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)\n+CHK\t7742088d\t2cf80e59\t99341a6a\n+# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.\n+SN\traw total sequences:\t641821\n+SN\tfiltered sequences:\t0\n+SN\tsequences:\t641821\n+SN\tis sorted:\t1\n+SN\t1st fragments:\t320981\n+SN\tlast fragments:\t320840\n+SN\treads mapped:\t641821\n+SN\treads mapped and paired:\t638746\t# paired-end technology bit set + both mates mapped\n+SN\treads unmapped:\t0\n+SN\treads properly paired:\t635626\t# proper-pair bit set\n+SN\treads paired:\t641821\t# paired-end technology bit set\n+SN\treads duplicated:\t0\t# PCR or optical duplicate bit set\n+SN\treads MQ0:\t70\t# mapped and MQ=0\n+SN\treads QC failed:\t0\n+SN\tnon-primary alignments:\t12111\n+SN\ttotal length:\t64823921\t# ignores clipping\n+SN\tbases mapped:\t64823921\t# ignores clipping\n+SN\tbases mapped (cigar):\t64823921\t# more accurate\n+SN\tbases trimmed:\t0\n+SN\tbases duplicated:\t0\n+SN\tmismatches:\t275405\t# from NM fields\n+SN\terror rate:\t4.248509e-03\t# mismatches / bases mapped (cigar)\n+SN\taverage length:\t101\n+SN\tmaximum length:\t101\n+SN\taverage quality:\t26.0\n+SN\tinsert size average:\t719.7\n+SN\tinsert size standard deviation:\t1223.0\n+SN\tinward oriented pairs:\t317512\n+SN\toutward oriented pairs:\t1294\n+SN\tpairs with other orientation:\t30\n+SN\tpairs on different chromosomes:\t0\n+# First Fragment Qualitites. Use `grep ^FFQ | cut -f 2-` to extract this part.\n+# Columns correspond to qualities and rows to cycles. First column is the cycle number.\n+FFQ\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t113\t0\t0\t0\t0\t320725\t143\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t4\t320810\t71\t91\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t3\t320877\t25\t75\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t5\t320905\t26\t44\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t8\t320816\t67\t86\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t0\t0\t0\t8\t320839\t42\t84\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t7\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t0\t0\t0\t6\t320867\t57\t47\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t8\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t8\t320845\t59\t64\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t9\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t2\t320851\t46\t78\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t10\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t4\t320836\t57\t77\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t11\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t7\t0\t0\t0\t0\t7\t320849\t46\t67\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t12\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t8\t320812\t80\t78\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t13\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t9\t320826\t56\t82\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t14\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t1\t0\t0\t0\t10\t320774\t77\t107\t7\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t15\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t8\t0\t0\t0\t0\t7\t320808\t60\t95\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t16\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t7\t1\t0\t0\t0\t12\t320786\t68\t101\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t17\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t8\t320758\t89\t116\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t18\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t6\t0\t0\t0\t0\t9\t320768\t86\t106\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t19\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t12\t320795\t77\t91\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t20\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t8\t0\t0\t0\t0\t11\t320739\t99\t110\t14\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t21\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t16\t320681\t115\t143\t21\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t22\t0\t0\t0\t0\t'..b'92-892]\t892\t9\n+COV\t[893-893]\t893\t9\n+COV\t[894-894]\t894\t12\n+COV\t[895-895]\t895\t16\n+COV\t[896-896]\t896\t10\n+COV\t[897-897]\t897\t8\n+COV\t[898-898]\t898\t8\n+COV\t[899-899]\t899\t11\n+COV\t[900-900]\t900\t7\n+COV\t[901-901]\t901\t15\n+COV\t[902-902]\t902\t13\n+COV\t[903-903]\t903\t17\n+COV\t[904-904]\t904\t9\n+COV\t[905-905]\t905\t8\n+COV\t[906-906]\t906\t13\n+COV\t[907-907]\t907\t10\n+COV\t[908-908]\t908\t8\n+COV\t[909-909]\t909\t13\n+COV\t[910-910]\t910\t7\n+COV\t[911-911]\t911\t9\n+COV\t[912-912]\t912\t8\n+COV\t[913-913]\t913\t9\n+COV\t[914-914]\t914\t8\n+COV\t[915-915]\t915\t9\n+COV\t[916-916]\t916\t6\n+COV\t[917-917]\t917\t9\n+COV\t[918-918]\t918\t7\n+COV\t[919-919]\t919\t9\n+COV\t[920-920]\t920\t8\n+COV\t[921-921]\t921\t13\n+COV\t[922-922]\t922\t5\n+COV\t[923-923]\t923\t5\n+COV\t[924-924]\t924\t5\n+COV\t[925-925]\t925\t7\n+COV\t[926-926]\t926\t10\n+COV\t[927-927]\t927\t6\n+COV\t[928-928]\t928\t21\n+COV\t[929-929]\t929\t10\n+COV\t[930-930]\t930\t10\n+COV\t[931-931]\t931\t7\n+COV\t[932-932]\t932\t12\n+COV\t[933-933]\t933\t14\n+COV\t[934-934]\t934\t14\n+COV\t[935-935]\t935\t7\n+COV\t[936-936]\t936\t12\n+COV\t[937-937]\t937\t13\n+COV\t[938-938]\t938\t10\n+COV\t[939-939]\t939\t12\n+COV\t[940-940]\t940\t18\n+COV\t[941-941]\t941\t11\n+COV\t[942-942]\t942\t10\n+COV\t[943-943]\t943\t6\n+COV\t[944-944]\t944\t12\n+COV\t[945-945]\t945\t12\n+COV\t[946-946]\t946\t8\n+COV\t[947-947]\t947\t12\n+COV\t[948-948]\t948\t10\n+COV\t[949-949]\t949\t5\n+COV\t[950-950]\t950\t9\n+COV\t[951-951]\t951\t16\n+COV\t[952-952]\t952\t13\n+COV\t[953-953]\t953\t15\n+COV\t[954-954]\t954\t15\n+COV\t[955-955]\t955\t8\n+COV\t[956-956]\t956\t15\n+COV\t[957-957]\t957\t18\n+COV\t[958-958]\t958\t9\n+COV\t[959-959]\t959\t21\n+COV\t[960-960]\t960\t14\n+COV\t[961-961]\t961\t17\n+COV\t[962-962]\t962\t9\n+COV\t[963-963]\t963\t14\n+COV\t[964-964]\t964\t6\n+COV\t[965-965]\t965\t5\n+COV\t[966-966]\t966\t13\n+COV\t[967-967]\t967\t12\n+COV\t[968-968]\t968\t13\n+COV\t[969-969]\t969\t10\n+COV\t[970-970]\t970\t13\n+COV\t[971-971]\t971\t8\n+COV\t[972-972]\t972\t13\n+COV\t[973-973]\t973\t12\n+COV\t[974-974]\t974\t14\n+COV\t[975-975]\t975\t9\n+COV\t[976-976]\t976\t12\n+COV\t[977-977]\t977\t4\n+COV\t[978-978]\t978\t14\n+COV\t[979-979]\t979\t6\n+COV\t[980-980]\t980\t12\n+COV\t[981-981]\t981\t5\n+COV\t[982-982]\t982\t8\n+COV\t[983-983]\t983\t4\n+COV\t[984-984]\t984\t9\n+COV\t[985-985]\t985\t9\n+COV\t[986-986]\t986\t10\n+COV\t[987-987]\t987\t8\n+COV\t[988-988]\t988\t4\n+COV\t[989-989]\t989\t6\n+COV\t[990-990]\t990\t3\n+COV\t[991-991]\t991\t5\n+COV\t[992-992]\t992\t2\n+COV\t[993-993]\t993\t6\n+COV\t[994-994]\t994\t6\n+COV\t[995-995]\t995\t7\n+COV\t[996-996]\t996\t14\n+COV\t[997-997]\t997\t12\n+COV\t[998-998]\t998\t7\n+COV\t[999-999]\t999\t8\n+COV\t[1000-1000]\t1000\t8\n+COV\t[1000<]\t1000\t5025\n+# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile\n+GCD\t0.0\t0.554\t0.000\t0.000\t0.000\t0.000\t0.000\n+GCD\t0.5\t0.831\t0.525\t0.525\t0.525\t0.525\t0.525\n+GCD\t36.0\t1.385\t0.954\t0.954\t0.954\t1.490\t1.490\n+GCD\t37.0\t2.216\t2.495\t2.495\t4.146\t6.560\t6.560\n+GCD\t38.0\t5.263\t0.247\t0.454\t3.520\t5.868\t9.883\n+GCD\t39.0\t9.141\t0.177\t0.303\t2.161\t8.777\t12.812\n+GCD\t40.0\t12.188\t0.020\t1.192\t9.060\t22.018\t27.371\n+GCD\t41.0\t16.343\t0.035\t0.550\t2.702\t11.469\t12.908\n+GCD\t42.0\t21.884\t0.010\t0.172\t2.121\t5.621\t17.094\n+GCD\t43.0\t28.255\t0.010\t0.328\t1.449\t4.277\t10.166\n+GCD\t44.0\t36.288\t0.162\t0.394\t5.484\t15.145\t50.490\n+GCD\t45.0\t42.105\t0.020\t0.131\t1.252\t7.009\t17.811\n+GCD\t46.0\t49.861\t0.015\t0.121\t0.636\t1.939\t37.506\n+GCD\t47.0\t56.510\t0.030\t0.141\t1.015\t4.500\t6.338\n+GCD\t48.0\t64.543\t0.010\t0.091\t2.565\t7.287\t21.872\n+GCD\t49.0\t68.975\t0.010\t0.333\t0.672\t10.751\t27.129\n+GCD\t50.0\t73.407\t0.010\t0.121\t1.358\t3.883\t6.615\n+GCD\t51.0\t77.008\t0.121\t0.576\t1.576\t4.363\t13.923\n+GCD\t52.0\t81.994\t0.010\t0.086\t1.560\t4.414\t109.383\n+GCD\t53.0\t84.488\t0.040\t0.071\t0.500\t3.025\t31.234\n+GCD\t54.0\t86.704\t0.020\t0.313\t9.332\t39.683\t203.959\n+GCD\t55.0\t89.197\t0.005\t0.051\t1.268\t5.045\t23.578\n+GCD\t56.0\t91.136\t0.071\t0.192\t1.566\t9.994\t33.315\n+GCD\t57.0\t94.460\t0.040\t0.348\t1.167\t5.050\t11.660\n+GCD\t58.0\t95.845\t0.131\t0.131\t1.899\t2.742\t4.929\n+GCD\t59.0\t96.399\t3.313\t3.313\t3.313\t3.666\t3.666\n+GCD\t60.0\t97.507\t0.995\t0.995\t5.176\t6.954\t33.234\n+GCD\t61.0\t98.338\t1.591\t1.591\t1.788\t4.848\t4.848\n+GCD\t62.0\t98.892\t3.171\t3.171\t3.171\t7.343\t7.343\n+GCD\t63.0\t99.446\t0.530\t0.530\t0.530\t6.403\t6.403\n+GCD\t64.0\t100.000\t1.025\t1.025\t1.025\t4.585\t4.585\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f multiqc/test-data/tophat_data.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc/test-data/tophat_data.txt Thu May 25 17:49:13 2017 -0400 |
| b |
| @@ -0,0 +1,14 @@ +Left reads: + Input : 316390 + Mapped : 314921 (99.5% of input) + of these: 5715 ( 1.8%) have multiple alignments (0 have >20) +Right reads: + Input : 316390 + Mapped : 314789 (99.5% of input) + of these: 5707 ( 1.8%) have multiple alignments (0 have >20) +99.5% overall read mapping rate. + +Aligned pairs: 313405 + of these: 5638 ( 1.8%) have multiple alignments + 34 ( 0.0%) are discordant alignments +99.0% concordant pair alignment rate. |
| b |
| diff -r 66f1187ed363 -r 4612d775965f readme.rst --- a/readme.rst Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,35 +0,0 @@ -======================== -Galaxy multiqc wrapper -======================== - -Aggregate results from bioinformatics analyses across many samples into a single report - -MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. - -============ -Installation -============ - -Requirements: pkg-config - -Conda recipe: A conda recipe exists in bioconda repository. If you have a recent Galaxy release, the packages installation is not mandatory. - -================ -MultiQC webpage -================ - -Important: For a good view of multiqc webpage, you need to deactivate the sanitize_all_html option in galaxy.ini - - sanitize_all_html = False - -======= -History -======= - - * v0.6: Initial public release - -========== -Citation -========== - -Created by EnginesOn company |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/CollectInsertSizeMetrics.txt --- a/test-data/CollectInsertSizeMetrics.txt Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,737 +0,0 @@ -## htsjdk.samtools.metrics.StringHeader -# picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=/omaha-beach/cloud_26/files/000/dataset_199.dat DEVIATIONS=10.0 MINIMUM_PCT=0.05 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=/omaha-beach/cloud_26/files/000/dataset_197.dat OUTPUT=/omaha-beach/cloud_26/files/000/dataset_198.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json -## htsjdk.samtools.metrics.StringHeader -# Started on: Mon May 23 09:33:00 UTC 2016 - -## METRICS CLASS picard.analysis.InsertSizeMetrics -MEDIAN_INSERT_SIZE MEDIAN_ABSOLUTE_DEVIATION MIN_INSERT_SIZE MAX_INSERT_SIZE MEAN_INSERT_SIZE STANDARD_DEVIATION READ_PAIRS PAIR_ORIENTATION WIDTH_OF_10_PERCENT WIDTH_OF_20_PERCENT WIDTH_OF_30_PERCENT WIDTH_OF_40_PERCENT WIDTH_OF_50_PERCENT WIDTH_OF_60_PERCENT WIDTH_OF_70_PERCENT WIDTH_OF_80_PERCENT WIDTH_OF_90_PERCENT WIDTH_OF_99_PERCENT SAMPLE LIBRARY READ_GROUP -194 63 100 5331452 271.809759 196.076488 311788 FR 25 47 69 91 127 343 941 1515 2585 16663 - -## HISTOGRAM java.lang.Integer -insert_size All_Reads.fr_count -100 2 -101 117 -102 424 -103 390 -104 376 -105 335 -106 360 -107 343 -108 353 -109 386 -110 349 -111 368 -112 445 -113 459 -114 470 -115 512 -116 478 -117 520 -118 558 -119 599 -120 603 -121 600 -122 696 -123 703 -124 657 -125 747 -126 734 -127 753 -128 820 -129 880 -130 923 -131 931 -132 953 -133 1006 -134 1086 -135 1134 -136 1177 -137 1280 -138 1381 -139 1419 -140 1494 -141 1625 -142 1697 -143 1838 -144 1899 -145 1957 -146 2197 -147 2214 -148 2276 -149 2450 -150 2557 -151 2523 -152 2619 -153 2591 -154 2575 -155 2745 -156 2756 -157 2716 -158 2765 -159 2775 -160 2884 -161 2830 -162 2781 -163 2718 -164 2777 -165 2859 -166 2803 -167 2855 -168 2896 -169 2817 -170 2843 -171 2817 -172 2844 -173 2855 -174 2777 -175 2684 -176 2703 -177 2574 -178 2516 -179 2569 -180 2494 -181 2374 -182 2322 -183 2186 -184 2117 -185 1992 -186 1914 -187 1831 -188 1883 -189 1705 -190 1610 -191 1484 -192 1484 -193 1358 -194 1290 -195 1180 -196 1148 -197 1013 -198 979 -199 895 -200 809 -201 715 -202 699 -203 616 -204 507 -205 501 -206 423 -207 374 -208 342 -209 301 -210 286 -211 180 -212 202 -213 175 -214 164 -215 134 -216 129 -217 93 -218 86 -219 89 -220 79 -221 66 -222 66 -223 57 -224 78 -225 67 -226 69 -227 70 -228 73 -229 82 -230 77 -231 85 -232 100 -233 109 -234 79 -235 96 -236 113 -237 100 -238 112 -239 106 -240 141 -241 141 -242 136 -243 133 -244 145 -245 136 -246 139 -247 150 -248 162 -249 157 -250 147 -251 170 -252 150 -253 180 -254 185 -255 187 -256 189 -257 181 -258 186 -259 188 -260 197 -261 199 -262 195 -263 183 -264 208 -265 192 -266 213 -267 215 -268 207 -269 192 -270 186 -271 189 -272 197 -273 188 -274 216 -275 203 -276 179 -277 209 -278 194 -279 202 -280 180 -281 177 -282 176 -283 173 -284 177 -285 167 -286 167 -287 181 -288 184 -289 190 -290 144 -291 161 -292 178 -293 173 -294 134 -295 151 -296 136 -297 145 -298 140 -299 144 -300 123 -301 121 -302 112 -303 103 -304 118 -305 110 -306 117 -307 126 -308 110 -309 95 -310 97 -311 105 -312 97 -313 98 -314 104 -315 81 -316 86 -317 83 -318 89 -319 78 -320 88 -321 89 -322 94 -323 84 -324 95 -325 86 -326 100 -327 97 -328 95 -329 186 -330 97 -331 74 -332 91 -333 79 -334 109 -335 101 -336 95 -337 100 -338 108 -339 94 -340 124 -341 102 -342 107 -343 103 -344 107 -345 114 -346 97 -347 109 -348 95 -349 115 -350 96 -351 101 -352 111 -353 121 -354 104 -355 109 -356 91 -357 129 -358 111 -359 126 -360 127 -361 123 -362 123 -363 101 -364 116 -365 114 -366 103 -367 115 -368 117 -369 110 -370 109 -371 108 -372 121 -373 111 -374 125 -375 121 -376 107 -377 101 -378 130 -379 103 -380 115 -381 92 -382 103 -383 101 -384 97 -385 114 -386 110 -387 94 -388 102 -389 90 -390 98 -391 82 -392 85 -393 86 -394 82 -395 86 -396 82 -397 111 -398 85 -399 90 -400 89 -401 95 -402 57 -403 105 -404 83 -405 69 -406 73 -407 79 -408 89 -409 66 -410 93 -411 81 -412 78 -413 71 -414 62 -415 71 -416 83 -417 69 -418 77 -419 76 -420 68 -421 73 -422 59 -423 74 -424 63 -425 72 -426 64 -427 72 -428 78 -429 69 -430 71 -431 74 -432 71 -433 62 -434 78 -435 80 -436 85 -437 77 -438 84 -439 72 -440 85 -441 84 -442 79 -443 65 -444 87 -445 81 -446 70 -447 77 -448 60 -449 66 -450 82 -451 88 -452 74 -453 97 -454 82 -455 86 -456 97 -457 107 -458 84 -459 91 -460 103 -461 88 -462 96 -463 82 -464 109 -465 104 -466 106 -467 103 -468 85 -469 102 -470 100 -471 106 -472 99 -473 101 -474 116 -475 104 -476 110 -477 103 -478 98 -479 95 -480 108 -481 111 -482 102 -483 118 -484 115 -485 113 -486 123 -487 111 -488 119 -489 120 -490 112 -491 115 -492 114 -493 114 -494 129 -495 117 -496 126 -497 113 -498 120 -499 114 -500 140 -501 108 -502 116 -503 110 -504 86 -505 127 -506 128 -507 119 -508 111 -509 122 -510 121 -511 155 -512 139 -513 141 -514 130 -515 132 -516 131 -517 132 -518 143 -519 146 -520 135 -521 141 -522 132 -523 141 -524 151 -525 144 -526 143 -527 155 -528 149 -529 149 -530 129 -531 129 -532 121 -533 139 -534 153 -535 141 -536 125 -537 136 -538 139 -539 128 -540 140 -541 107 -542 114 -543 138 -544 138 -545 140 -546 113 -547 132 -548 145 -549 139 -550 139 -551 107 -552 131 -553 119 -554 117 -555 132 -556 125 -557 197 -558 118 -559 115 -560 127 -561 111 -562 115 -563 110 -564 117 -565 114 -566 113 -567 115 -568 127 -569 113 -570 107 -571 111 -572 97 -573 112 -574 110 -575 108 -576 110 -577 108 -578 113 -579 104 -580 78 -581 101 -582 121 -583 97 -584 111 -585 107 -586 98 -587 107 -588 94 -589 113 -590 110 -591 107 -592 114 -593 118 -594 100 -595 116 -596 98 -597 107 -598 90 -599 114 -600 107 -601 117 -602 109 -603 103 -604 107 -605 122 -606 112 -607 106 -608 114 -609 101 -610 95 -611 106 -612 107 -613 101 -614 115 -615 88 -616 113 -617 101 -618 103 -619 114 -620 110 -621 126 -622 108 -623 112 -624 111 -625 121 -626 116 -627 106 -628 111 -629 93 -630 103 -631 96 -632 98 -633 80 -634 104 -635 86 -636 88 -637 102 -638 89 -639 78 -640 85 -641 109 -642 106 -643 80 -644 86 -645 93 -646 76 -647 81 -648 91 -649 92 -650 100 -651 88 -652 73 -653 97 -654 111 -655 76 -656 99 -657 90 -658 92 -659 87 -660 101 -661 103 -662 91 -663 105 -664 102 -665 89 -666 84 -667 104 -668 95 -669 99 -670 106 -671 101 -672 103 -673 111 -674 94 -675 108 -676 93 -677 113 -678 101 -679 86 -680 102 -681 97 -682 91 -683 107 -684 102 -685 112 -686 112 -687 98 -688 102 -689 112 -690 116 -691 90 -692 90 -693 96 -694 100 -695 85 -696 101 -697 106 -698 92 -699 90 -700 97 -701 102 -702 105 -703 109 -704 122 -705 101 -706 123 -707 126 -708 115 -709 114 -710 99 -711 136 -712 102 -713 114 -714 114 -715 119 -716 105 -717 121 -718 140 -719 113 -720 124 -721 140 -722 102 -723 146 -724 118 -725 145 -726 133 -727 155 -728 149 -729 129 -730 146 -731 153 -732 155 -733 164 -734 162 -735 179 -736 162 -737 158 -738 161 -739 171 -740 171 -741 168 -742 161 -743 198 -744 185 -745 146 -746 161 -747 178 -748 184 -749 185 -750 179 -751 189 -752 187 -753 166 -754 179 -755 170 -756 181 -757 193 -758 185 -759 201 -760 202 -761 195 -762 176 -763 204 -764 201 -765 182 -766 183 -767 180 -768 161 -769 174 -770 173 -771 185 -772 160 -773 180 -774 170 -775 167 -776 187 -777 167 -778 179 -779 187 -780 157 -781 176 -782 162 -783 158 -784 161 -785 160 -786 177 -787 161 -788 174 -789 145 -790 143 -791 148 -792 162 -793 170 -794 145 -795 157 -796 132 -797 150 -798 149 -799 131 -800 158 -801 132 -802 128 -803 118 -804 107 -805 120 -806 132 -807 122 -808 108 -809 116 -810 133 -811 112 -812 125 -813 93 -814 94 -815 94 -816 101 -817 91 -818 94 -819 98 -820 82 -821 73 -822 87 -823 69 -824 84 - |
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| diff -r 66f1187ed363 -r 4612d775965f test-data/MarkDuplicates_data.txt --- a/test-data/MarkDuplicates_data.txt Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,112 +0,0 @@ -## htsjdk.samtools.metrics.StringHeader -# picard.sam.markduplicates.MarkDuplicates INPUT=[/omaha-beach/cloud_26/files/000/dataset_114.dat] OUTPUT=/omaha-beach/cloud_26/files/000/dataset_197.dat METRICS_FILE=/omaha-beach/cloud_26/files/000/dataset_196.dat REMOVE_DUPLICATES=false ASSUME_SORTED=true DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json -## htsjdk.samtools.metrics.StringHeader -# Started on: Mon May 23 09:32:41 UTC 2016 - -## METRICS CLASS picard.sam.DuplicationMetrics -LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE -Unknown Library 2900 313405 0 2257 629 0 0.005582 77973949 - -## HISTOGRAM java.lang.Double -BIN VALUE -1.0 1 -2.0 1.995989 -3.0 2.987982 -4.0 3.975997 -5.0 4.960048 -6.0 5.940152 -7.0 6.916324 -8.0 7.88858 -9.0 8.856937 -10.0 9.821409 -11.0 10.782013 -12.0 11.738763 -13.0 12.691676 -14.0 13.640766 -15.0 14.586049 -16.0 15.52754 -17.0 16.465254 -18.0 17.399207 -19.0 18.329414 -20.0 19.25589 -21.0 20.178649 -22.0 21.097706 -23.0 22.013077 -24.0 22.924776 -25.0 23.832819 -26.0 24.737218 -27.0 25.63799 -28.0 26.535149 -29.0 27.428709 -30.0 28.318684 -31.0 29.20509 -32.0 30.08794 -33.0 30.967248 -34.0 31.84303 -35.0 32.715298 -36.0 33.584068 -37.0 34.449352 -38.0 35.311166 -39.0 36.169523 -40.0 37.024436 -41.0 37.875921 -42.0 38.723989 -43.0 39.568656 -44.0 40.409935 -45.0 41.247839 -46.0 42.082382 -47.0 42.913578 -48.0 43.741439 -49.0 44.565979 -50.0 45.387212 -51.0 46.205151 -52.0 47.019809 -53.0 47.831199 -54.0 48.639334 -55.0 49.444228 -56.0 50.245893 -57.0 51.044342 -58.0 51.839588 -59.0 52.631645 -60.0 53.420524 -61.0 54.206239 -62.0 54.988802 -63.0 55.768226 -64.0 56.544524 -65.0 57.317707 -66.0 58.087789 -67.0 58.854783 -68.0 59.618699 -69.0 60.379551 -70.0 61.137352 -71.0 61.892112 -72.0 62.643845 -73.0 63.392562 -74.0 64.138276 -75.0 64.880999 -76.0 65.620743 -77.0 66.357519 -78.0 67.09134 -79.0 67.822217 -80.0 68.550163 -81.0 69.275188 -82.0 69.997306 -83.0 70.716526 -84.0 71.432862 -85.0 72.146324 -86.0 72.856924 -87.0 73.564674 -88.0 74.269585 -89.0 74.971668 -90.0 75.670935 -91.0 76.367397 -92.0 77.061066 -93.0 77.751952 -94.0 78.440066 -95.0 79.12542 -96.0 79.808025 -97.0 80.487892 -98.0 81.165032 -99.0 81.839456 -100.0 82.511174 - |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/bismark_data.txt --- a/test-data/bismark_data.txt Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,39 +0,0 @@ -Bismark report for: /omaha-beach/cloud_26/files/000/dataset_33.dat (version: v0.10.0) -Option '--directional' specified: alignments to complementary strands will be ignored (i.e. not performed!) -Bowtie was run against the bisulfite genome of /root/galaxy/database/tmp/tmpvNBPSF/ with the specified options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet - -Final Alignment report -====================== -Sequences analysed in total: 316390 -Number of alignments with a unique best hit from the different alignments: 220558 -Mapping efficiency: 69.7% -Sequences with no alignments under any condition: 93928 -Sequences did not map uniquely: 1904 -Sequences which were discarded because genomic sequence could not be extracted: 0 - -Number of sequences with unique best (first) alignment came from the bowtie output: -CT/CT: 108352 ((converted) top strand) -CT/GA: 112206 ((converted) bottom strand) -GA/CT: 0 (complementary to (converted) top strand) -GA/GA: 0 (complementary to (converted) bottom strand) - -Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 - -Final Cytosine Methylation Report -================================= -Total number of C's analysed: 5291918 - -Total methylated C's in CpG context: 465068 -Total methylated C's in CHG context: 1358074 -Total methylated C's in CHH context: 3449120 -Total methylated C's in Unknown context: 1499 - -Total unmethylated C's in CpG context: 6399 -Total unmethylated C's in CHG context: 2988 -Total unmethylated C's in CHH context: 10269 -Total unmethylated C's in Unknown context: 454 - -C methylated in CpG context: 98.6% -C methylated in CHG context: 99.8% -C methylated in CHH context: 99.7% -C methylated in Unknown context (CN or CHN): 76.8% |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/collectGcBias_data.txt --- a/test-data/collectGcBias_data.txt Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,110 +0,0 @@ -## htsjdk.samtools.metrics.StringHeader -# picard.analysis.CollectGcBiasMetrics CHART_OUTPUT=/omaha-beach/cloud_26/files/000/dataset_195.dat SUMMARY_OUTPUT=/omaha-beach/cloud_26/files/000/dataset_193.dat WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=5.0E-5 IS_BISULFITE_SEQUENCED=true INPUT=/omaha-beach/cloud_26/files/000/dataset_114.dat OUTPUT=/omaha-beach/cloud_26/files/000/dataset_194.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa METRIC_ACCUMULATION_LEVEL=[ALL_READS] STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json -## htsjdk.samtools.metrics.StringHeader -# Started on: Mon May 23 09:32:30 UTC 2016 - -## METRICS CLASS picard.analysis.GcBiasDetailMetrics -ACCUMULATION_LEVEL GC WINDOWS READ_STARTS MEAN_BASE_QUALITY NORMALIZED_COVERAGE ERROR_BAR_WIDTH SAMPLE LIBRARY READ_GROUP -All Reads 0 0 0 0 0 0 -All Reads 1 0 0 0 0 0 -All Reads 2 0 0 0 0 0 -All Reads 3 10 0 0 0 0 -All Reads 4 7 0 0 0 0 -All Reads 5 6 0 0 0 0 -All Reads 6 4 0 0 0 0 -All Reads 7 9 0 0 0 0 -All Reads 8 22 0 0 0 0 -All Reads 9 15 0 0 0 0 -All Reads 10 20 0 0 0 0 -All Reads 11 18 0 0 0 0 -All Reads 12 101 0 0 0 0 -All Reads 13 118 0 0 0 0 -All Reads 14 137 1 20 0.110575 0.110575 -All Reads 15 243 4 19 0.249362 0.124681 -All Reads 16 366 10 21 0.4139 0.130887 -All Reads 17 468 9 24 0.291322 0.097107 -All Reads 18 689 25 24 0.549664 0.109933 -All Reads 19 1087 40 26 0.557451 0.088141 -All Reads 20 2152 95 25 0.668741 0.068611 -All Reads 21 3279 127 23 0.586731 0.052064 -All Reads 22 5106 178 23 0.528099 0.039583 -All Reads 23 7817 319 23 0.618197 0.034612 -All Reads 24 11933 630 24 0.799774 0.031864 -All Reads 25 17449 759 25 0.658943 0.023918 -All Reads 26 25272 1414 26 0.847591 0.02254 -All Reads 27 34926 1806 25 0.783331 0.018433 -All Reads 28 48489 2889 26 0.90257 0.016792 -All Reads 29 64950 4285 26 0.99942 0.015268 -All Reads 30 84452 5453 26 0.978142 0.013246 -All Reads 31 107535 6476 26 0.912291 0.011337 -All Reads 32 134982 7953 26 0.892548 0.010008 -All Reads 33 165941 9475 26 0.864972 0.008886 -All Reads 34 199087 11437 26 0.870253 0.008137 -All Reads 35 233144 12856 26 0.83533 0.007367 -All Reads 36 266049 14918 26 0.849426 0.006955 -All Reads 37 298999 17019 26 0.862265 0.00661 -All Reads 38 327958 20230 26 0.934446 0.00657 -All Reads 39 350801 22684 26 0.97957 0.006504 -All Reads 40 369841 23670 26 0.969527 0.006302 -All Reads 41 383262 25527 26 1.008975 0.006315 -All Reads 42 392470 26131 25 1.008617 0.006239 -All Reads 43 395234 25603 25 0.981326 0.006133 -All Reads 44 392428 26425 25 1.020074 0.006275 -All Reads 45 386569 25213 25 0.988039 0.006222 -All Reads 46 376763 25980 25 1.044594 0.006481 -All Reads 47 363422 24801 25 1.033795 0.006564 -All Reads 48 348339 24838 25 1.080167 0.006854 -All Reads 49 331960 24992 24 1.140491 0.007214 -All Reads 50 315781 23793 24 1.141405 0.0074 -All Reads 51 297249 22601 24 1.151818 0.007662 -All Reads 52 278159 19653 24 1.070317 0.007635 -All Reads 53 263713 19395 24 1.114127 0.008 -All Reads 54 247317 19047 24 1.166673 0.008453 -All Reads 55 230663 17922 23 1.177023 0.008792 -All Reads 56 215458 16244 23 1.142107 0.008961 -All Reads 57 198515 14904 23 1.137329 0.009316 -All Reads 58 180718 13720 23 1.150083 0.009819 -All Reads 59 165914 11940 23 1.090179 0.009977 -All Reads 60 152561 10775 23 1.069917 0.010307 -All Reads 61 138857 9746 23 1.063249 0.01077 -All Reads 62 125804 9067 22 1.091807 0.011466 -All Reads 63 112222 7148 22 0.964902 0.011413 -All Reads 64 99218 6056 23 0.924638 0.011882 -All Reads 65 85414 5612 24 0.995326 0.013286 -All Reads 66 72999 4286 23 0.88943 0.013586 -All Reads 67 61396 3631 23 0.895907 0.014868 -All Reads 68 52109 3341 22 0.971271 0.016804 -All Reads 69 45121 2735 21 0.918238 0.017558 -All Reads 70 38925 1675 21 0.651873 0.015928 -All Reads 71 32225 1053 22 0.495008 0.015254 -All Reads 72 27537 721 22 0.396639 0.014772 -All Reads 73 23481 483 22 0.311607 0.014179 -All Reads 74 20300 423 22 0.315661 0.015348 -All Reads 75 17785 245 22 0.208684 0.013332 -All Reads 76 15846 236 22 0.225615 0.014686 -All Reads 77 13683 230 22 0.254638 0.01679 -All Reads 78 11733 217 23 0.280174 0.019019 -All Reads 79 10547 188 22 0.270026 0.019694 -All Reads 80 9314 151 22 0.245594 0.019986 -All Reads 81 7659 149 23 0.294707 0.024143 -All Reads 82 5813 56 25 0.145937 0.019502 -All Reads 83 4687 46 23 0.148676 0.021921 -All Reads 84 3505 18 23 0.077797 0.018337 -All Reads 85 2385 8 23 0.050813 0.017965 -All Reads 86 1424 5 21 0.053191 0.023788 -All Reads 87 859 3 20 0.052906 0.030545 -All Reads 88 529 0 0 0 0 -All Reads 89 411 0 0 0 0 -All Reads 90 348 0 0 0 0 -All Reads 91 138 0 0 0 0 -All Reads 92 40 0 0 0 0 -All Reads 93 7 0 0 0 0 -All Reads 94 7 0 0 0 0 -All Reads 95 12 0 0 0 0 -All Reads 96 17 0 0 0 0 -All Reads 97 8 0 0 0 0 -All Reads 98 9 0 0 0 0 -All Reads 99 5 0 0 0 0 -All Reads 100 30 0 0 0 0 - - |
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| diff -r 66f1187ed363 -r 4612d775965f test-data/cutadapt.txt --- a/test-data/cutadapt.txt Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,129 +0,0 @@ -You are running cutadapt 1.6 with Python 2.7.3 -Command line parameters: --format=fastq --anywhere=fakadaptater=CACG --error-rate=0.1 --times=1 --overlap=3 --output=/omaha-beach/cloud_26/files/000/dataset_82.dat /omaha-beach/cloud_26/files/000/dataset_33.dat -Maximum error rate: 10.00% - No. of adapters: 1 - Processed reads: 316390 - Processed bases: 31955390 bp (32.0 Mbp) - Trimmed reads: 68795 (21.7%) - Trimmed bases: 3443775 bp (3.4 Mbp) (10.78% of total) - Too short reads: 0 (0.0% of processed reads) - Too long reads: 0 (0.0% of processed reads) - Total time: 5.28 s - Time per read: 0.017 ms - -=== Adapter 'fakadaptater' === - -Sequence: CACG; Length: 4; Trimmed: 68795 times. -2162 times, it overlapped the 5' end of a read -66633 times, it overlapped the 3' end or was within the read - -No. of allowed errors: -0-4 bp: 0 - -Overview of removed sequences (5') -length count expect max.err error counts -3 357 4943.6 0 357 -4 1805 1235.9 0 1805 - - -Overview of removed sequences (3' or within) -length count expect max.err error counts -3 4175 4943.6 0 4175 -4 520 1235.9 0 520 -5 442 1235.9 0 442 -6 522 1235.9 0 522 -7 538 1235.9 0 538 -8 526 1235.9 0 526 -9 482 1235.9 0 482 -10 547 1235.9 0 547 -11 502 1235.9 0 502 -12 539 1235.9 0 539 -13 571 1235.9 0 571 -14 601 1235.9 0 601 -15 537 1235.9 0 537 -16 592 1235.9 0 592 -17 604 1235.9 0 604 -18 617 1235.9 0 617 -19 594 1235.9 0 594 -20 493 1235.9 0 493 -21 558 1235.9 0 558 -22 503 1235.9 0 503 -23 573 1235.9 0 573 -24 609 1235.9 0 609 -25 653 1235.9 0 653 -26 625 1235.9 0 625 -27 541 1235.9 0 541 -28 501 1235.9 0 501 -29 618 1235.9 0 618 -30 539 1235.9 0 539 -31 614 1235.9 0 614 -32 594 1235.9 0 594 -33 627 1235.9 0 627 -34 572 1235.9 0 572 -35 690 1235.9 0 690 -36 615 1235.9 0 615 -37 654 1235.9 0 654 -38 681 1235.9 0 681 -39 530 1235.9 0 530 -40 731 1235.9 0 731 -41 622 1235.9 0 622 -42 611 1235.9 0 611 -43 722 1235.9 0 722 -44 664 1235.9 0 664 -45 659 1235.9 0 659 -46 651 1235.9 0 651 -47 591 1235.9 0 591 -48 642 1235.9 0 642 -49 545 1235.9 0 545 -50 573 1235.9 0 573 -51 591 1235.9 0 591 -52 567 1235.9 0 567 -53 749 1235.9 0 749 -54 647 1235.9 0 647 -55 753 1235.9 0 753 -56 696 1235.9 0 696 -57 780 1235.9 0 780 -58 607 1235.9 0 607 -59 758 1235.9 0 758 -60 643 1235.9 0 643 -61 578 1235.9 0 578 -62 670 1235.9 0 670 -63 652 1235.9 0 652 -64 816 1235.9 0 816 -65 732 1235.9 0 732 -66 640 1235.9 0 640 -67 644 1235.9 0 644 -68 818 1235.9 0 818 -69 658 1235.9 0 658 -70 587 1235.9 0 587 -71 672 1235.9 0 672 -72 588 1235.9 0 588 -73 645 1235.9 0 645 -74 668 1235.9 0 668 -75 725 1235.9 0 725 -76 651 1235.9 0 651 -77 701 1235.9 0 701 -78 662 1235.9 0 662 -79 655 1235.9 0 655 -80 760 1235.9 0 760 -81 746 1235.9 0 746 -82 705 1235.9 0 705 -83 704 1235.9 0 704 -84 726 1235.9 0 726 -85 692 1235.9 0 692 -86 700 1235.9 0 700 -87 758 1235.9 0 758 -88 640 1235.9 0 640 -89 665 1235.9 0 665 -90 848 1235.9 0 848 -91 693 1235.9 0 693 -92 775 1235.9 0 775 -93 1237 1235.9 0 1237 -94 629 1235.9 0 629 -95 574 1235.9 0 574 -96 525 1235.9 0 525 -97 586 1235.9 0 586 -98 696 1235.9 0 696 -99 860 1235.9 0 860 -100 851 1235.9 0 851 - |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/fastqc_data.txt --- a/test-data/fastqc_data.txt Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,2181 +0,0 @@\n-##FastQC\t0.11.4\n->>Basic Statistics\tpass\n-#Measure\tValue\n-Filename\tpoulet5_1\n-File type\tConventional base calls\n-Encoding\tSanger / Illumina 1.9\n-Total Sequences\t267849\n-Sequences flagged as poor quality\t0\n-Sequence length\t101\n-%GC\t48\n->>END_MODULE\n->>Per base sequence quality\twarn\n-#Base\tMean\tMedian\tLower Quartile\tUpper Quartile\t10th Percentile\t90th Percentile\n-1\t20.91988023102569\t21.0\t21.0\t21.0\t21.0\t21.0\n-2\t20.71684045861661\t21.0\t20.0\t22.0\t19.0\t23.0\n-3\t20.351574954545285\t21.0\t20.0\t21.0\t18.0\t22.0\n-4\t22.531542025544244\t23.0\t22.0\t24.0\t20.0\t24.0\n-5\t24.673566076408722\t25.0\t24.0\t26.0\t24.0\t26.0\n-6\t25.813099918237516\t26.0\t25.0\t27.0\t25.0\t27.0\n-7\t27.587864804423386\t28.0\t27.0\t29.0\t26.0\t29.0\n-8\t27.598941941168345\t28.0\t27.0\t29.0\t26.0\t29.0\n-9\t27.07115949658203\t28.0\t26.0\t28.0\t26.0\t28.0\n-10-11\t27.129873548155864\t28.0\t26.0\t28.0\t25.5\t28.0\n-12-13\t27.009298149330405\t27.5\t26.0\t28.0\t25.5\t28.0\n-14-15\t27.123565889736383\t28.0\t26.5\t28.0\t26.0\t28.0\n-16-17\t27.086309823818645\t28.0\t26.0\t28.0\t26.0\t28.0\n-18-19\t27.07924614241606\t28.0\t26.0\t28.0\t25.5\t28.0\n-20-21\t27.082520375286073\t28.0\t26.0\t28.0\t26.0\t28.0\n-22-23\t27.054301117420636\t28.0\t26.0\t28.0\t25.0\t28.0\n-24-25\t27.06350966402712\t28.0\t26.0\t28.0\t25.0\t28.0\n-26-27\t27.082996389756914\t28.0\t26.0\t28.0\t26.0\t28.0\n-28-29\t27.065495857740743\t28.0\t26.0\t28.0\t25.5\t28.0\n-30-31\t27.09608772106672\t28.0\t26.0\t28.0\t26.0\t28.0\n-32-33\t27.087097581099798\t28.0\t26.0\t28.0\t26.0\t28.0\n-34-35\t27.098251253504774\t28.0\t26.5\t28.0\t26.0\t28.0\n-36-37\t27.05184077595959\t28.0\t26.0\t28.0\t25.5\t28.0\n-38-39\t27.06521958267531\t28.0\t26.0\t28.0\t26.0\t28.0\n-40-41\t27.072148859992012\t28.0\t26.0\t28.0\t26.0\t28.0\n-42-43\t27.065725464720796\t28.0\t26.0\t28.0\t25.5\t28.0\n-44-45\t27.07168031241483\t28.0\t26.5\t28.0\t25.5\t28.0\n-46-47\t27.048083061725073\t28.0\t26.0\t28.0\t25.5\t28.0\n-48-49\t27.04642354460909\t28.0\t26.0\t28.0\t25.5\t28.0\n-50-51\t27.062865644448927\t28.0\t26.0\t28.0\t25.5\t28.0\n-52-53\t27.01859629866081\t28.0\t26.0\t28.0\t25.0\t28.0\n-54-55\t26.994157155710866\t27.5\t26.0\t28.0\t25.0\t28.0\n-56-57\t27.110127347871376\t28.0\t27.0\t28.0\t26.0\t28.0\n-58-59\t26.995846540401494\t27.5\t26.0\t28.0\t25.0\t28.0\n-60-61\t27.00461640700544\t27.5\t26.0\t28.0\t25.0\t28.0\n-62-63\t26.981614641085088\t27.5\t26.5\t28.0\t25.5\t28.5\n-64-65\t26.98900313236189\t28.0\t26.0\t28.0\t25.0\t28.0\n-66-67\t27.001189102815392\t28.0\t26.0\t28.0\t25.0\t28.0\n-68-69\t26.917739099268616\t27.5\t26.0\t28.0\t25.0\t28.5\n-70-71\t26.98481793846533\t28.0\t27.0\t28.0\t25.0\t29.0\n-72-73\t26.89518908041471\t27.5\t26.5\t28.0\t25.0\t28.5\n-74-75\t26.93677034448514\t28.0\t27.0\t28.0\t25.0\t29.0\n-76-77\t26.87640237596556\t28.0\t26.5\t28.0\t25.0\t29.0\n-78-79\t26.906094478605482\t28.0\t27.0\t28.0\t25.0\t29.0\n-80-81\t26.80463992772047\t28.0\t26.5\t28.0\t25.0\t29.0\n-82-83\t26.717012197170796\t28.0\t26.5\t28.0\t25.0\t29.0\n-84-85\t26.46960974280285\t27.5\t26.5\t28.0\t25.0\t29.0\n-86-87\t26.442842795754324\t27.5\t26.5\t28.0\t25.0\t29.0\n-88-89\t26.34282375517549\t28.0\t26.0\t28.0\t25.0\t29.0\n-90-91\t26.03493946215965\t28.0\t26.0\t28.0\t24.5\t29.0\n-92-93\t25.833215729758187\t28.0\t26.0\t28.0\t24.0\t29.0\n-94-95\t25.503102494315826\t27.5\t26.0\t28.0\t22.5\t29.0\n-96-97\t24.52807178671565\t27.0\t25.5\t27.5\t21.0\t28.0\n-98-99\t23.202399486277717\t26.0\t24.5\t26.5\t10.0\t27.0\n-100-101\t23.72906749698524\t27.0\t26.0\t28.0\t2.0\t29.0\n->>END_MODULE\n->>Per tile sequence quality\tpass\n-#Tile\tBase\tMean\n-1101\t1\t0.017259946109469126\n-1101\t2\t-0.13408255940416325\n-1101\t3\t-0.11853598095770224\n-1101\t4\t0.015421063929771606\n-1101\t5\t-0.06886052494072459\n-1101\t6\t-0.15241701542762698\n-1101\t7\t-0.029853727500473326\n-1101\t8\t0.04533865186875374\n-1101\t9\t0.07102084333114078\n-1101\t10-11\t0.02726717483210095\n-1101\t12-13\t0.05147474989913192\n-1101\t14-15\t-0.006227419450461014\n-1101\t16-17\t0.051879075943595865\n-1101\t18-19\t0.03525737425918152\n-1101\t20-21\t0.012963832365290529\n-1101\t22-23\t0.02506089814612622\n-1101\t24-25\t0.07843149833360386\n-1101\t26-27\t0.02737786083297422\n-1101\t28-29\t0.005161107012540356\n-1101\t30-31\t-0.08720467946375265\n-1101\t32-33\t-0.017197404032327057\n-1101\t34-35\t0.05763469947927646\n-1101\t36-37\t-0.045600552109540615\n-1101\t38-39\t-0.01952943529413176\n-1101\t40-41\t0.007678874836642535\n-1101\t42-43\t-0.00844'..b'433.5\n-55\t9922.0\n-56\t8785.5\n-57\t7997.0\n-58\t6901.0\n-59\t5796.0\n-60\t4967.0\n-61\t4072.5\n-62\t3639.5\n-63\t3267.0\n-64\t2561.5\n-65\t2002.5\n-66\t1561.5\n-67\t1355.5\n-68\t1222.0\n-69\t1019.0\n-70\t803.0\n-71\t568.5\n-72\t371.5\n-73\t235.0\n-74\t164.5\n-75\t110.5\n-76\t70.5\n-77\t56.0\n-78\t39.5\n-79\t27.0\n-80\t18.0\n-81\t17.0\n-82\t15.5\n-83\t12.5\n-84\t6.5\n-85\t1.5\n-86\t0.0\n-87\t0.0\n-88\t0.0\n-89\t0.0\n-90\t0.0\n-91\t0.0\n-92\t0.0\n-93\t0.0\n-94\t0.0\n-95\t0.0\n-96\t0.0\n-97\t0.0\n-98\t0.0\n-99\t0.0\n-100\t0.0\n->>END_MODULE\n->>Per base N content\tpass\n-#Base\tN-Count\n-1\t0.029867574640935753\n-2\t0.0\n-3\t0.003733446830116969\n-4\t0.0\n-5\t3.733446830116969E-4\n-6\t0.0\n-7\t0.0\n-8\t0.0\n-9\t0.0\n-10-11\t0.0\n-12-13\t0.0\n-14-15\t0.0\n-16-17\t0.0\n-18-19\t0.0\n-20-21\t0.0\n-22-23\t0.0\n-24-25\t0.0\n-26-27\t0.0\n-28-29\t0.0\n-30-31\t0.0\n-32-33\t0.0\n-34-35\t0.0\n-36-37\t0.0\n-38-39\t0.0\n-40-41\t0.0\n-42-43\t0.0\n-44-45\t0.0\n-46-47\t0.0\n-48-49\t0.0\n-50-51\t0.0\n-52-53\t0.0\n-54-55\t0.0\n-56-57\t0.0\n-58-59\t0.0\n-60-61\t0.0\n-62-63\t0.0\n-64-65\t0.0\n-66-67\t0.0\n-68-69\t0.0\n-70-71\t0.0\n-72-73\t0.0\n-74-75\t0.0\n-76-77\t0.0\n-78-79\t0.0\n-80-81\t0.0\n-82-83\t0.0\n-84-85\t0.0\n-86-87\t0.0\n-88-89\t0.0\n-90-91\t0.0\n-92-93\t0.0\n-94-95\t0.0\n-96-97\t0.0\n-98-99\t0.0\n-100-101\t0.0\n->>END_MODULE\n->>Sequence Length Distribution\tpass\n-#Length\tCount\n-101\t267849.0\n->>END_MODULE\n->>Sequence Duplication Levels\twarn\n-#Total Deduplicated Percentage\t63.69408840068983\n-#Duplication Level\tPercentage of deduplicated\tPercentage of total\n-1\t81.5623716290639\t51.950409087115126\n-2\t9.995611185249079\t12.733226849043577\n-3\t3.1947144335386772\t6.104532706343167\n-4\t1.4905270052149588\t3.797510353351082\n-5\t0.8725392208870194\t2.778779513412342\n-6\t0.55360835935223\t2.115694786796508\n-7\t0.38537193434967776\t1.718213983752925\n-8\t0.314619574221819\t1.603152557845755\n-9\t0.2033036957962869\t1.1654319215012086\n->10\t1.4223398099582591\t15.850860027094066\n->50\t0.0049931523680946535\t0.18218821374420768\n->100\t0.0\t0.0\n->500\t0.0\t0.0\n->1k\t0.0\t0.0\n->5k\t0.0\t0.0\n->10k+\t0.0\t0.0\n->>END_MODULE\n->>Overrepresented sequences\tpass\n->>END_MODULE\n->>Adapter Content\tpass\n-#Position\tIllumina Universal Adapter\tIllumina Small RNA Adapter\tNextera Transposase Sequence\tSOLID Small RNA Adapter\n-1\t0.0\t0.0\t0.0\t0.0\n-2\t0.0\t0.0\t0.0\t0.0\n-3\t0.0\t0.0\t0.0\t0.0\n-4\t0.0\t0.0\t0.0\t0.0\n-5\t0.0\t0.0\t0.0\t0.0\n-6\t0.0\t0.0\t0.0\t0.0\n-7\t0.0\t0.0\t0.0\t0.0\n-8\t0.0\t0.0\t0.0\t0.0\n-9\t0.0\t0.0\t0.0\t0.0\n-10-11\t0.0\t0.0\t0.0\t0.0\n-12-13\t0.0\t0.0\t0.0\t0.0\n-14-15\t0.0\t0.0\t0.0\t0.0\n-16-17\t0.0\t0.0\t0.0\t0.0\n-18-19\t0.0\t0.0\t0.0\t0.0\n-20-21\t0.0\t0.0\t0.0\t0.0\n-22-23\t0.0\t0.0\t0.0\t0.0\n-24-25\t0.0\t0.0\t0.0\t0.0\n-26-27\t0.0\t0.0\t0.0\t0.0\n-28-29\t0.0\t0.0\t0.0\t0.0\n-30-31\t0.0\t0.0\t0.0\t0.0\n-32-33\t0.0\t0.0\t0.0\t0.0\n-34-35\t0.0\t0.0\t0.0\t0.0\n-36-37\t0.0\t0.0\t0.0\t0.0\n-38-39\t0.0\t0.0\t0.0\t0.0\n-40-41\t0.0\t0.0\t0.0\t0.0\n-42-43\t0.0\t0.0\t0.0\t0.0\n-44-45\t0.0\t0.0\t0.0\t0.0\n-46-47\t0.0\t0.0\t0.0\t0.0\n-48-49\t0.0\t0.0\t0.0\t0.0\n-50-51\t0.0\t0.0\t0.0\t0.0\n-52-53\t0.0\t0.0\t0.0\t0.0\n-54-55\t0.0\t0.0\t0.0\t0.0\n-56-57\t0.0\t0.0\t0.0\t0.0\n-58-59\t0.0\t0.0\t0.0\t0.0\n-60-61\t0.0\t0.0\t0.0\t0.0\n-62-63\t0.0\t0.0\t0.0\t0.0\n-64-65\t0.0\t0.0\t0.0\t0.0\n-66-67\t0.0\t0.0\t0.0\t0.0\n-68-69\t0.0\t0.0\t0.0\t0.0\n-70-71\t0.0\t0.0\t0.0\t0.0\n-72-73\t0.0\t0.0\t0.0\t0.0\n-74-75\t0.0\t0.0\t0.0\t0.0\n-76-77\t0.0\t0.0\t0.0\t0.0\n-78-79\t0.0\t0.0\t0.0\t0.0\n-80-81\t0.0\t0.0\t0.0\t0.0\n-82-83\t0.0\t0.0\t0.0\t0.0\n-84-85\t0.0\t0.0\t0.0\t0.0\n-86-87\t0.0\t0.0\t0.0\t0.0\n-88-89\t0.0\t0.0\t0.0\t0.0\n->>END_MODULE\n->>Kmer Content\twarn\n-#Sequence\tCount\tPValue\tObs/Exp Max\tMax Obs/Exp Position\n-TTAGTGG\t50\t0.0016122013\t38.00672\t3\n-CCGGGAA\t65\t0.0058204937\t29.246862\t1\n-CTCGCCA\t65\t0.0058204937\t29.246862\t1\n-CCCGCTT\t70\t0.008357804\t27.157803\t1\n-AACAATT\t125\t0.006013185\t19.00336\t2\n-CTGGGAT\t205\t3.3062082E-4\t16.228443\t1\n-AGTTCAA\t195\t0.0044498937\t14.615241\t5\n-GAGTAGT\t125\t0.0014974214\t13.29987\t30-31\n-AAGTTCA\t220\t0.009890434\t12.954418\t4\n-CTGAAAT\t275\t0.003044474\t12.097567\t1\n-CCCAGCT\t405\t3.2130985E-5\t11.734852\t1\n-AGGGTGT\t145\t0.0045575905\t11.465405\t66-67\n-CTGAATT\t335\t0.001024679\t11.349529\t1\n-CTTGAAT\t295\t0.0051441877\t11.277392\t1\n-GAATGTC\t425\t6.555659E-4\t10.058724\t4\n-GGTAGTA\t190\t0.002949709\t9.999902\t52-53\n-CTCTGCC\t390\t0.0036302158\t9.748955\t1\n-CTCCTTT\t535\t5.356131E-4\t8.883393\t1\n-CTTTGCT\t500\t0.0028739348\t8.5547085\t1\n->>END_MODULE\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/fastqc_data_2.txt --- a/test-data/fastqc_data_2.txt Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,2170 +0,0 @@\n-##FastQC\t0.11.4\n->>Basic Statistics\tpass\n-#Measure\tValue\n-Filename\tpoulet5_2\n-File type\tConventional base calls\n-Encoding\tSanger / Illumina 1.9\n-Total Sequences\t267849\n-Sequences flagged as poor quality\t0\n-Sequence length\t101\n-%GC\t48\n->>END_MODULE\n->>Per base sequence quality\twarn\n-#Base\tMean\tMedian\tLower Quartile\tUpper Quartile\t10th Percentile\t90th Percentile\n-1\t20.590586487162543\t21.0\t21.0\t21.0\t20.0\t21.0\n-2\t20.458478471078855\t21.0\t19.0\t22.0\t19.0\t22.0\n-3\t20.178608096352797\t21.0\t20.0\t21.0\t18.0\t22.0\n-4\t22.495204387546714\t23.0\t22.0\t24.0\t20.0\t24.0\n-5\t24.59397272343746\t25.0\t24.0\t26.0\t24.0\t26.0\n-6\t25.77560491172265\t26.0\t25.0\t27.0\t25.0\t27.0\n-7\t26.651378201897337\t27.0\t26.0\t28.0\t26.0\t28.0\n-8\t27.54968284369178\t28.0\t27.0\t29.0\t26.0\t29.0\n-9\t27.089005372429988\t28.0\t26.0\t28.0\t26.0\t28.0\n-10-11\t27.058984726469017\t28.0\t26.0\t28.0\t25.5\t28.0\n-12-13\t26.954911162632676\t27.5\t26.0\t28.0\t25.5\t28.0\n-14-15\t27.066410552214123\t28.0\t26.0\t28.0\t26.0\t28.0\n-16-17\t27.04552938409328\t28.0\t26.0\t28.0\t25.5\t28.0\n-18-19\t27.025118630273028\t28.0\t26.0\t28.0\t25.0\t28.0\n-20-21\t27.019042445557012\t28.0\t26.0\t28.0\t25.0\t28.0\n-22-23\t27.010315513591614\t28.0\t26.0\t28.0\t25.0\t28.0\n-24-25\t27.03931879529138\t28.0\t26.0\t28.0\t25.5\t28.0\n-26-27\t26.978450544896567\t28.0\t26.0\t28.0\t25.0\t28.0\n-28-29\t27.003714779595967\t28.0\t26.0\t28.0\t25.0\t28.0\n-30-31\t27.025971722873706\t28.0\t26.0\t28.0\t25.0\t28.0\n-32-33\t27.017791740868923\t28.0\t26.0\t28.0\t25.0\t28.0\n-34-35\t27.00628899118533\t28.0\t26.0\t28.0\t25.0\t28.0\n-36-37\t27.00906294218011\t28.0\t26.0\t28.0\t25.0\t28.0\n-38-39\t27.034922661648913\t28.0\t26.0\t28.0\t25.5\t28.0\n-40-41\t27.005346295860726\t28.0\t26.0\t28.0\t25.0\t28.0\n-42-43\t27.000909094303132\t28.0\t26.0\t28.0\t25.0\t28.0\n-44-45\t27.004913216028434\t28.0\t26.0\t28.0\t25.0\t28.0\n-46-47\t26.979999925331065\t28.0\t26.0\t28.0\t25.0\t28.0\n-48-49\t26.941037674211962\t27.5\t26.0\t28.0\t25.0\t28.0\n-50-51\t26.99995146519121\t27.5\t26.0\t28.0\t25.5\t28.0\n-52-53\t26.95084543903468\t27.5\t26.0\t28.0\t25.0\t28.0\n-54-55\t26.97609847339359\t28.0\t26.0\t28.0\t25.0\t28.0\n-56-57\t26.99262270906369\t27.5\t26.0\t28.0\t25.0\t28.0\n-58-59\t26.942271578389317\t27.0\t26.0\t28.0\t25.0\t28.0\n-60-61\t26.88024222603034\t27.0\t26.0\t28.0\t25.0\t28.0\n-62-63\t26.866450873439888\t27.0\t26.0\t28.0\t25.0\t28.0\n-64-65\t26.947610407356386\t28.0\t26.0\t28.0\t25.0\t28.0\n-66-67\t26.975012040366025\t28.0\t26.5\t28.0\t25.0\t28.5\n-68-69\t26.966286975124042\t28.0\t26.5\t28.0\t25.0\t29.0\n-70-71\t26.917634562757375\t28.0\t26.0\t28.0\t25.0\t29.0\n-72-73\t26.885127441207544\t28.0\t26.0\t28.0\t25.0\t29.0\n-74-75\t26.846286527110426\t28.0\t26.5\t28.0\t25.0\t29.0\n-76-77\t26.769134848366058\t28.0\t26.0\t28.0\t25.0\t29.0\n-78-79\t26.709703975000842\t28.0\t26.5\t28.0\t25.0\t29.0\n-80-81\t26.551336760637525\t27.5\t26.0\t28.0\t25.0\t28.5\n-82-83\t26.42626069165836\t27.5\t26.0\t28.0\t25.0\t28.5\n-84-85\t26.309463541024982\t27.5\t26.0\t28.0\t25.0\t29.0\n-86-87\t26.127226534353312\t27.5\t26.0\t28.0\t25.0\t29.0\n-88-89\t25.91885539987082\t27.5\t26.0\t28.0\t24.0\t29.0\n-90-91\t25.674260497519125\t27.0\t26.0\t28.0\t23.5\t29.0\n-92-93\t25.371903572535274\t27.0\t26.0\t28.0\t22.0\t29.0\n-94-95\t24.758753999454918\t27.0\t26.0\t28.0\t20.5\t28.5\n-96-97\t23.84710415196622\t26.5\t25.0\t27.5\t7.0\t28.0\n-98-99\t22.40618968149965\t25.5\t24.0\t26.5\t2.0\t27.0\n-100-101\t23.009550156991438\t27.0\t25.0\t28.0\t2.0\t29.0\n->>END_MODULE\n->>Per tile sequence quality\tpass\n-#Tile\tBase\tMean\n-1101\t1\t-0.1408369887985721\n-1101\t2\t-0.019030947201084558\n-1101\t3\t-0.060059442415557385\n-1101\t4\t0.004085939732711097\n-1101\t5\t-0.018429270835582656\n-1101\t6\t-0.10404524639907464\n-1101\t7\t0.05541229462318498\n-1101\t8\t0.06703529503928962\n-1101\t9\t0.0644374620344621\n-1101\t10-11\t0.06977859906234585\n-1101\t12-13\t0.048103685880093394\n-1101\t14-15\t0.0848396420659725\n-1101\t16-17\t0.030233298636137107\n-1101\t18-19\t0.05253119669850648\n-1101\t20-21\t0.08961672433820667\n-1101\t22-23\t0.014190195653434046\n-1101\t24-25\t-0.013817302849609803\n-1101\t26-27\t0.046003756870838686\n-1101\t28-29\t0.04599618351544166\n-1101\t30-31\t0.04851104267937956\n-1101\t32-33\t0.04656194043190354\n-1101\t34-35\t0.057517795385400916\n-1101\t36-37\t-0.00326392946157128\n-1101\t38-39\t0.0753296536157606\n-1101\t40-41\t0.005995075411309614\n-1101\t42-43\t-0.013913'..b'71.0\n-24\t130.0\n-25\t233.5\n-26\t389.5\n-27\t542.5\n-28\t724.5\n-29\t1063.0\n-30\t1433.0\n-31\t1683.5\n-32\t1996.0\n-33\t2367.5\n-34\t2840.5\n-35\t3318.0\n-36\t3924.5\n-37\t4721.0\n-38\t5510.0\n-39\t6259.0\n-40\t7364.0\n-41\t8736.0\n-42\t9608.5\n-43\t10256.0\n-44\t10928.5\n-45\t11153.5\n-46\t11271.5\n-47\t12042.0\n-48\t12804.5\n-49\t12874.0\n-50\t12482.5\n-51\t11758.0\n-52\t10827.0\n-53\t10433.0\n-54\t10615.0\n-55\t9955.0\n-56\t8760.0\n-57\t7986.5\n-58\t6982.5\n-59\t5802.5\n-60\t4913.5\n-61\t4177.5\n-62\t3751.5\n-63\t3282.0\n-64\t2533.0\n-65\t1954.0\n-66\t1513.0\n-67\t1247.5\n-68\t1102.0\n-69\t957.0\n-70\t777.0\n-71\t535.5\n-72\t361.5\n-73\t253.0\n-74\t157.0\n-75\t99.0\n-76\t60.0\n-77\t46.5\n-78\t37.0\n-79\t21.5\n-80\t13.5\n-81\t16.5\n-82\t19.5\n-83\t14.0\n-84\t6.5\n-85\t3.0\n-86\t0.5\n-87\t0.0\n-88\t0.0\n-89\t0.0\n-90\t0.0\n-91\t0.0\n-92\t0.0\n-93\t0.0\n-94\t0.0\n-95\t0.0\n-96\t0.0\n-97\t0.0\n-98\t0.0\n-99\t0.0\n-100\t0.0\n->>END_MODULE\n->>Per base N content\tpass\n-#Base\tN-Count\n-1\t0.11461681768459094\n-2\t0.003733446830116969\n-3\t0.0\n-4\t0.0\n-5\t0.0\n-6\t0.0\n-7\t0.0\n-8\t0.0\n-9\t0.0\n-10-11\t0.0\n-12-13\t0.0\n-14-15\t0.0\n-16-17\t0.0\n-18-19\t0.0\n-20-21\t0.0\n-22-23\t0.0\n-24-25\t0.0\n-26-27\t0.0\n-28-29\t0.0\n-30-31\t0.0\n-32-33\t0.0\n-34-35\t0.0\n-36-37\t0.0\n-38-39\t0.0\n-40-41\t0.0\n-42-43\t0.0\n-44-45\t0.0\n-46-47\t0.0\n-48-49\t0.0\n-50-51\t0.0\n-52-53\t0.0\n-54-55\t0.0\n-56-57\t0.0\n-58-59\t0.0\n-60-61\t0.0\n-62-63\t0.0\n-64-65\t0.0\n-66-67\t0.0\n-68-69\t0.0\n-70-71\t0.0\n-72-73\t0.0\n-74-75\t0.0\n-76-77\t0.0\n-78-79\t0.0\n-80-81\t0.0\n-82-83\t1.8667234150584845E-4\n-84-85\t0.0\n-86-87\t1.8667234150584845E-4\n-88-89\t0.0014933787320467876\n-90-91\t0.0\n-92-93\t0.0011200340490350907\n-94-95\t0.0\n-96-97\t0.0\n-98-99\t0.0\n-100-101\t0.01456044263745618\n->>END_MODULE\n->>Sequence Length Distribution\tpass\n-#Length\tCount\n-101\t267849.0\n->>END_MODULE\n->>Sequence Duplication Levels\twarn\n-#Total Deduplicated Percentage\t63.826611251945884\n-#Duplication Level\tPercentage of deduplicated\tPercentage of total\n-1\t81.66283073871745\t52.122617512935754\n-2\t9.894108596885154\t12.630148461958491\n-3\t3.18062640137576\t6.090258145748586\n-4\t1.5566170090070461\t3.974143548082379\n-5\t0.8538567368205473\t2.7249391002950074\n-6\t0.5533319107768025\t2.119038045746843\n-7\t0.3960736941041749\t1.7696029190496514\n-8\t0.2698969625036296\t1.3781286803040145\n-9\t0.23212846037984958\t1.3334375701059644\n->10\t1.3969694370078172\t15.730893862039416\n->50\t0.0035600524217624095\t0.12679215373389083\n->100\t0.0\t0.0\n->500\t0.0\t0.0\n->1k\t0.0\t0.0\n->5k\t0.0\t0.0\n->10k+\t0.0\t0.0\n->>END_MODULE\n->>Overrepresented sequences\tpass\n->>END_MODULE\n->>Adapter Content\tpass\n-#Position\tIllumina Universal Adapter\tIllumina Small RNA Adapter\tNextera Transposase Sequence\tSOLID Small RNA Adapter\n-1\t0.0\t0.0\t0.0\t0.0\n-2\t0.0\t0.0\t0.0\t0.0\n-3\t0.0\t0.0\t0.0\t0.0\n-4\t0.0\t0.0\t0.0\t0.0\n-5\t0.0\t0.0\t0.0\t0.0\n-6\t0.0\t0.0\t0.0\t0.0\n-7\t0.0\t0.0\t0.0\t0.0\n-8\t0.0\t0.0\t0.0\t0.0\n-9\t0.0\t0.0\t0.0\t0.0\n-10-11\t0.0\t0.0\t0.0\t0.0\n-12-13\t0.0\t0.0\t0.0\t0.0\n-14-15\t0.0\t0.0\t0.0\t0.0\n-16-17\t0.0\t0.0\t0.0\t0.0\n-18-19\t0.0\t0.0\t0.0\t0.0\n-20-21\t0.0\t0.0\t0.0\t0.0\n-22-23\t0.0\t0.0\t0.0\t0.0\n-24-25\t0.0\t0.0\t0.0\t0.0\n-26-27\t0.0\t0.0\t0.0\t0.0\n-28-29\t0.0\t0.0\t0.0\t0.0\n-30-31\t0.0\t0.0\t0.0\t0.0\n-32-33\t0.0\t0.0\t0.0\t0.0\n-34-35\t0.0\t0.0\t0.0\t0.0\n-36-37\t0.0\t0.0\t0.0\t0.0\n-38-39\t0.0\t0.0\t0.0\t0.0\n-40-41\t0.0\t0.0\t0.0\t0.0\n-42-43\t0.0\t0.0\t0.0\t0.0\n-44-45\t0.0\t0.0\t0.0\t0.0\n-46-47\t0.0\t0.0\t0.0\t0.0\n-48-49\t0.0\t0.0\t0.0\t0.0\n-50-51\t0.0\t0.0\t0.0\t0.0\n-52-53\t0.0\t0.0\t0.0\t0.0\n-54-55\t0.0\t0.0\t0.0\t0.0\n-56-57\t0.0\t0.0\t0.0\t0.0\n-58-59\t0.0\t0.0\t0.0\t0.0\n-60-61\t0.0\t0.0\t0.0\t0.0\n-62-63\t0.0\t0.0\t0.0\t0.0\n-64-65\t0.0\t0.0\t0.0\t0.0\n-66-67\t0.0\t0.0\t0.0\t0.0\n-68-69\t0.0\t0.0\t0.0\t0.0\n-70-71\t0.0\t0.0\t0.0\t0.0\n-72-73\t0.0\t0.0\t0.0\t0.0\n-74-75\t0.0\t0.0\t0.0\t0.0\n-76-77\t0.0\t0.0\t0.0\t0.0\n-78-79\t0.0\t0.0\t0.0\t0.0\n-80-81\t0.0\t0.0\t0.0\t0.0\n-82-83\t0.0\t0.0\t0.0\t0.0\n-84-85\t0.0\t0.0\t0.0\t0.0\n-86-87\t0.0\t0.0\t0.0\t0.0\n-88-89\t0.0\t0.0\t0.0\t0.0\n->>END_MODULE\n->>Kmer Content\twarn\n-#Sequence\tCount\tPValue\tObs/Exp Max\tMax Obs/Exp Position\n-TACGAGG\t60\t0.0039460836\t31.665857\t9\n-CCCAGAT\t105\t6.861368E-5\t27.157375\t1\n-AATCAAC\t70\t0.008381328\t27.142164\t5\n-CTTGTAT\t120\t0.004739449\t19.802252\t1\n-TCGCTCA\t130\t0.007549489\t18.268764\t2\n-CCCCACT\t195\t0.0044338168\t14.623201\t1\n-TTCAACA\t295\t0.005166332\t11.270898\t2\n-CTTGAAG\t305\t0.006593838\t10.90747\t1\n->>END_MODULE\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/featurecounts_data.txt --- a/test-data/featurecounts_data.txt Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,12 +0,0 @@ -Status 70: TopHat on data 1, data 4, and data 3: accepted_hits 75: TopHat on data 1, data 6, and data 5: accepted_hits 80: TopHat on data 1, data 8, and data 7: accepted_hits 85: TopHat on data 1, data 10, and data 9: accepted_hits 90: TopHat on data 1, data 12, and data 11: accepted_hits 95: TopHat on data 1, data 14, and data 13: accepted_hits -Assigned 321797 445012 394981 437485 388170 453929 -Unassigned_Ambiguity 2333 3424 3121 3692 2782 3554 -Unassigned_MultiMapping 19123 25293 22580 19907 21164 23533 -Unassigned_NoFeatures 111117 165786 129664 146327 132063 160805 -Unassigned_Unmapped 0 0 0 0 0 0 -Unassigned_MappingQuality 0 0 0 0 0 0 -Unassigned_FragmentLength 0 0 0 0 0 0 -Unassigned_Chimera 0 0 0 0 0 0 -Unassigned_Secondary 0 0 0 0 0 0 -Unassigned_Nonjunction 0 0 0 0 0 0 -Unassigned_Duplicate 0 0 0 0 0 0 |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/log_all.txt --- a/test-data/log_all.txt Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,47 +0,0 @@ -[2016-05-23 10:05:37,586] multiqc [INFO ] This is MultiQC v0.6 -[2016-05-23 10:05:37,587] multiqc [DEBUG ] Command : /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/bin/multiqc multiqc_WDir -[2016-05-23 10:05:37,587] multiqc [DEBUG ] Working dir : /root/galaxy/database/jobs_directory/000/107/working -[2016-05-23 10:05:37,587] multiqc [DEBUG ] Template : default -[2016-05-23 10:05:37,587] multiqc [DEBUG ] No MultiQC config found: /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/lib/python/multiqc-0.6-py2.7.egg/multiqc_config.yaml -[2016-05-23 10:05:37,587] multiqc [DEBUG ] No MultiQC config found: /root/.multiqc_config.yaml -[2016-05-23 10:05:37,587] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml -[2016-05-23 10:05:37,744] multiqc [INFO ] Searching 'multiqc_WDir' -[2016-05-23 10:05:37,744] multiqc [DEBUG ] Analysing modules: snpeff, qualimap, featureCounts, methylQA, rseqc, picard, preseq, samblaster, samtools, bamtools, bismark, hicup, salmon, star, tophat, bowtie2, bowtie1, cutadapt, trimmomatic, skewer, fastq_screen, fastqc -[2016-05-23 10:05:37,744] multiqc [DEBUG ] Using temporary directory for creating report: /root/galaxy/database/tmp/tmpmeCIjG -[2016-05-23 10:05:37,752] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 10:05:37,754] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 10:05:37,757] multiqc.modules.featureCounts.feature_counts [INFO ] Found 6 reports -[2016-05-23 10:05:37,760] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 10:05:37,839] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 10:05:37,987] multiqc.modules.picard.picard [INFO ] Found 1 dupMetrics reports -[2016-05-23 10:05:37,988] multiqc.modules.picard.picard [INFO ] Found 1 insertSize reports -[2016-05-23 10:05:37,993] multiqc.modules.picard.picard [INFO ] Found 1 GCbias reports -[2016-05-23 10:05:38,017] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',) -[2016-05-23 10:05:38,042] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 10:05:38,079] multiqc.modules.samtools.samtools [INFO ] Found 1 reports -[2016-05-23 10:05:38,104] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 10:05:38,111] multiqc.modules.bismark.bismark [INFO ] Found 1 bismark alignment reports -[2016-05-23 10:05:38,114] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('multiqc_WDir',) -[2016-05-23 10:05:38,116] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('multiqc_WDir',) -[2016-05-23 10:05:38,118] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 10:05:38,121] multiqc.modules.tophat.tophat [INFO ] Found 1 reports -[2016-05-23 10:05:38,146] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 10:05:38,170] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 10:05:38,196] multiqc.modules.cutadapt.cutadapt [INFO ] Found 1 reports -[2016-05-23 10:05:38,221] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('multiqc_WDir',) -[2016-05-23 10:05:38,244] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 10:05:38,246] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 10:05:38,313] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports -[2016-05-23 10:05:38,318] multiqc [INFO ] Report : multiqc_report.html -[2016-05-23 10:05:38,318] multiqc [INFO ] Data : multiqc_data -[2016-05-23 10:05:38,319] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpmeCIjG/multiqc_data/multiqc_fastqc.txt' to '/root/galaxy/database/jobs_directory/000/107/working/multiqc_data' -[2016-05-23 10:05:38,319] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpmeCIjG/multiqc_data/multiqc_picard_dups.txt' to '/root/galaxy/database/jobs_directory/000/107/working/multiqc_data' -[2016-05-23 10:05:38,319] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpmeCIjG/multiqc_data/multiqc_bismark_alignment.txt' to '/root/galaxy/database/jobs_directory/000/107/working/multiqc_data' -[2016-05-23 10:05:38,319] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpmeCIjG/multiqc_data/multiqc_cutadapt.txt' to '/root/galaxy/database/jobs_directory/000/107/working/multiqc_data' -[2016-05-23 10:05:38,319] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpmeCIjG/multiqc_data/multiqc_general_stats.txt' to '/root/galaxy/database/jobs_directory/000/107/working/multiqc_data' -[2016-05-23 10:05:38,319] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpmeCIjG/multiqc_data/multiqc_samtools.txt' to '/root/galaxy/database/jobs_directory/000/107/working/multiqc_data' -[2016-05-23 10:05:38,319] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpmeCIjG/multiqc_data/multiqc_picard_insertSize.txt' to '/root/galaxy/database/jobs_directory/000/107/working/multiqc_data' -[2016-05-23 10:05:38,320] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpmeCIjG/multiqc_data/multiqc_sources.txt' to '/root/galaxy/database/jobs_directory/000/107/working/multiqc_data' -[2016-05-23 10:05:38,320] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpmeCIjG/multiqc_data/multiqc_featureCounts.txt' to '/root/galaxy/database/jobs_directory/000/107/working/multiqc_data' -[2016-05-23 10:05:38,320] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpmeCIjG/multiqc_data/multiqc_tophat.txt.txt' to '/root/galaxy/database/jobs_directory/000/107/working/multiqc_data' -[2016-05-23 10:05:38,395] multiqc [INFO ] MultiQC complete |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/log_bismark.txt --- a/test-data/log_bismark.txt Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,44 +0,0 @@ -[2016-05-23 09:52:41,602] multiqc [INFO ] This is MultiQC v0.6 -[2016-05-23 09:52:41,602] multiqc [DEBUG ] Command : /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/bin/multiqc multiqc_WDir -[2016-05-23 09:52:41,602] multiqc [DEBUG ] Working dir : /root/galaxy/database/jobs_directory/000/104/working -[2016-05-23 09:52:41,602] multiqc [DEBUG ] Template : default -[2016-05-23 09:52:41,602] multiqc [DEBUG ] No MultiQC config found: /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/lib/python/multiqc-0.6-py2.7.egg/multiqc_config.yaml -[2016-05-23 09:52:41,602] multiqc [DEBUG ] No MultiQC config found: /root/.multiqc_config.yaml -[2016-05-23 09:52:41,603] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml -[2016-05-23 09:52:41,732] multiqc [INFO ] Searching 'multiqc_WDir' -[2016-05-23 09:52:41,732] multiqc [DEBUG ] Analysing modules: snpeff, qualimap, featureCounts, methylQA, rseqc, picard, preseq, samblaster, samtools, bamtools, bismark, hicup, salmon, star, tophat, bowtie2, bowtie1, cutadapt, trimmomatic, skewer, fastq_screen, fastqc -[2016-05-23 09:52:41,732] multiqc [DEBUG ] Using temporary directory for creating report: /root/galaxy/database/tmp/tmpJtZqxl -[2016-05-23 09:52:41,739] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 09:52:41,743] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:52:41,746] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:52:41,748] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:52:41,756] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:52:41,760] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:52:41,762] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',) -[2016-05-23 09:52:41,765] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 09:52:41,768] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:52:41,771] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:52:41,779] multiqc.modules.bismark.bismark [INFO ] Found 1 bismark alignment reports -[2016-05-23 09:52:41,783] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('multiqc_WDir',) -[2016-05-23 09:52:41,786] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('multiqc_WDir',) -[2016-05-23 09:52:41,789] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:52:41,792] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:52:41,794] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:52:41,797] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:52:41,800] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:52:41,803] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('multiqc_WDir',) -[2016-05-23 09:52:41,806] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 09:52:41,809] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:52:41,812] multiqc.modules.fastqc.fastqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:52:41,812] multiqc.plots.table [DEBUG ] Removing header percent_cpg_meth from general stats table, as no data -[2016-05-23 09:52:41,812] multiqc.plots.table [DEBUG ] Removing header percent_chg_meth from general stats table, as no data -[2016-05-23 09:52:41,812] multiqc.plots.table [DEBUG ] Removing header percent_chh_meth from general stats table, as no data -[2016-05-23 09:52:41,813] multiqc.plots.table [DEBUG ] Removing header total_c from general stats table, as no data -[2016-05-23 09:52:41,813] multiqc.plots.table [DEBUG ] Removing header dup_reads_percent from general stats table, as no data -[2016-05-23 09:52:41,813] multiqc.plots.table [DEBUG ] Removing header dedup_reads from general stats table, as no data -[2016-05-23 09:52:41,813] multiqc [INFO ] Report : multiqc_report.html -[2016-05-23 09:52:41,813] multiqc [INFO ] Data : multiqc_data -[2016-05-23 09:52:41,814] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpJtZqxl/multiqc_data/multiqc_bismark_alignment.txt' to '/root/galaxy/database/jobs_directory/000/104/working/multiqc_data' -[2016-05-23 09:52:41,814] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpJtZqxl/multiqc_data/multiqc_general_stats.txt' to '/root/galaxy/database/jobs_directory/000/104/working/multiqc_data' -[2016-05-23 09:52:41,814] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpJtZqxl/multiqc_data/multiqc_sources.txt' to '/root/galaxy/database/jobs_directory/000/104/working/multiqc_data' -[2016-05-23 09:52:41,907] multiqc [INFO ] MultiQC complete |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/log_cutadapt.txt --- a/test-data/log_cutadapt.txt Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,39 +0,0 @@ -[2016-05-23 10:04:17,236] multiqc [INFO ] This is MultiQC v0.6 -[2016-05-23 10:04:17,236] multiqc [DEBUG ] Command : /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/bin/multiqc multiqc_WDir -[2016-05-23 10:04:17,236] multiqc [DEBUG ] Working dir : /root/galaxy/database/jobs_directory/000/106/working -[2016-05-23 10:04:17,236] multiqc [DEBUG ] Template : default -[2016-05-23 10:04:17,236] multiqc [DEBUG ] No MultiQC config found: /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/lib/python/multiqc-0.6-py2.7.egg/multiqc_config.yaml -[2016-05-23 10:04:17,236] multiqc [DEBUG ] No MultiQC config found: /root/.multiqc_config.yaml -[2016-05-23 10:04:17,236] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml -[2016-05-23 10:04:17,383] multiqc [INFO ] Searching 'multiqc_WDir' -[2016-05-23 10:04:17,383] multiqc [DEBUG ] Analysing modules: snpeff, qualimap, featureCounts, methylQA, rseqc, picard, preseq, samblaster, samtools, bamtools, bismark, hicup, salmon, star, tophat, bowtie2, bowtie1, cutadapt, trimmomatic, skewer, fastq_screen, fastqc -[2016-05-23 10:04:17,383] multiqc [DEBUG ] Using temporary directory for creating report: /root/galaxy/database/tmp/tmpqOU4l7 -[2016-05-23 10:04:17,390] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 10:04:17,392] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 10:04:17,394] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 10:04:17,395] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 10:04:17,400] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 10:04:17,403] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 10:04:17,405] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',) -[2016-05-23 10:04:17,406] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 10:04:17,408] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 10:04:17,410] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 10:04:17,413] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 10:04:17,414] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('multiqc_WDir',) -[2016-05-23 10:04:17,416] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('multiqc_WDir',) -[2016-05-23 10:04:17,418] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 10:04:17,420] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 10:04:17,422] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 10:04:17,424] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 10:04:17,429] multiqc.modules.cutadapt.cutadapt [INFO ] Found 1 reports -[2016-05-23 10:04:17,431] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('multiqc_WDir',) -[2016-05-23 10:04:17,433] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 10:04:17,435] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 10:04:17,437] multiqc.modules.fastqc.fastqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 10:04:17,437] multiqc.plots.table [DEBUG ] Removing header percent_trimmed from general stats table, as no data -[2016-05-23 10:04:17,438] multiqc [INFO ] Report : multiqc_report.html -[2016-05-23 10:04:17,438] multiqc [INFO ] Data : multiqc_data -[2016-05-23 10:04:17,438] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpqOU4l7/multiqc_data/multiqc_cutadapt.txt' to '/root/galaxy/database/jobs_directory/000/106/working/multiqc_data' -[2016-05-23 10:04:17,438] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpqOU4l7/multiqc_data/multiqc_general_stats.txt' to '/root/galaxy/database/jobs_directory/000/106/working/multiqc_data' -[2016-05-23 10:04:17,438] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpqOU4l7/multiqc_data/multiqc_sources.txt' to '/root/galaxy/database/jobs_directory/000/106/working/multiqc_data' -[2016-05-23 10:04:17,517] multiqc [INFO ] MultiQC complete |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/log_fastqc.txt --- a/test-data/log_fastqc.txt Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,38 +0,0 @@ -[2016-05-23 08:53:43,440] multiqc [INFO ] This is MultiQC v0.6 -[2016-05-23 08:53:43,440] multiqc [DEBUG ] Command : /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/bin/multiqc multiqc_WDir -[2016-05-23 08:53:43,440] multiqc [DEBUG ] Working dir : /root/galaxy/database/jobs_directory/000/87/working -[2016-05-23 08:53:43,440] multiqc [DEBUG ] Template : default -[2016-05-23 08:53:43,440] multiqc [DEBUG ] No MultiQC config found: /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/lib/python/multiqc-0.6-py2.7.egg/multiqc_config.yaml -[2016-05-23 08:53:43,441] multiqc [DEBUG ] No MultiQC config found: /root/.multiqc_config.yaml -[2016-05-23 08:53:43,441] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml -[2016-05-23 08:53:43,564] multiqc [INFO ] Searching 'multiqc_WDir' -[2016-05-23 08:53:43,564] multiqc [DEBUG ] Analysing modules: snpeff, qualimap, featureCounts, methylQA, rseqc, picard, preseq, samblaster, samtools, bamtools, bismark, hicup, salmon, star, tophat, bowtie2, bowtie1, cutadapt, trimmomatic, skewer, fastq_screen, fastqc -[2016-05-23 08:53:43,564] multiqc [DEBUG ] Using temporary directory for creating report: /root/galaxy/database/tmp/tmpzTj1_Q -[2016-05-23 08:53:43,571] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 08:53:43,573] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:53:43,575] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:53:43,576] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:53:43,589] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:53:43,605] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:53:43,609] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',) -[2016-05-23 08:53:43,614] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 08:53:43,618] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:53:43,623] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:53:43,625] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:53:43,627] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('multiqc_WDir',) -[2016-05-23 08:53:43,629] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('multiqc_WDir',) -[2016-05-23 08:53:43,631] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:53:43,633] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:53:43,637] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:53:43,642] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:53:43,646] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:53:43,651] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('multiqc_WDir',) -[2016-05-23 08:53:43,655] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 08:53:43,657] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:53:43,697] multiqc.modules.fastqc.fastqc [INFO ] Found 1 reports -[2016-05-23 08:53:43,702] multiqc [INFO ] Report : multiqc_report.html -[2016-05-23 08:53:43,702] multiqc [INFO ] Data : multiqc_data -[2016-05-23 08:53:43,702] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpzTj1_Q/multiqc_data/multiqc_fastqc.txt' to '/root/galaxy/database/jobs_directory/000/87/working/multiqc_data' -[2016-05-23 08:53:43,702] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpzTj1_Q/multiqc_data/multiqc_general_stats.txt' to '/root/galaxy/database/jobs_directory/000/87/working/multiqc_data' -[2016-05-23 08:53:43,702] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpzTj1_Q/multiqc_data/multiqc_sources.txt' to '/root/galaxy/database/jobs_directory/000/87/working/multiqc_data' -[2016-05-23 08:53:43,780] multiqc [INFO ] MultiQC complete |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/log_fastqc_2.txt --- a/test-data/log_fastqc_2.txt Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,38 +0,0 @@ -[2016-05-23 08:57:23,478] multiqc [INFO ] This is MultiQC v0.6 -[2016-05-23 08:57:23,478] multiqc [DEBUG ] Command : /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/bin/multiqc multiqc_WDir -[2016-05-23 08:57:23,478] multiqc [DEBUG ] Working dir : /root/galaxy/database/jobs_directory/000/88/working -[2016-05-23 08:57:23,478] multiqc [DEBUG ] Template : default -[2016-05-23 08:57:23,478] multiqc [DEBUG ] No MultiQC config found: /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/lib/python/multiqc-0.6-py2.7.egg/multiqc_config.yaml -[2016-05-23 08:57:23,479] multiqc [DEBUG ] No MultiQC config found: /root/.multiqc_config.yaml -[2016-05-23 08:57:23,479] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml -[2016-05-23 08:57:23,642] multiqc [INFO ] Searching 'multiqc_WDir' -[2016-05-23 08:57:23,642] multiqc [DEBUG ] Analysing modules: snpeff, qualimap, featureCounts, methylQA, rseqc, picard, preseq, samblaster, samtools, bamtools, bismark, hicup, salmon, star, tophat, bowtie2, bowtie1, cutadapt, trimmomatic, skewer, fastq_screen, fastqc -[2016-05-23 08:57:23,642] multiqc [DEBUG ] Using temporary directory for creating report: /root/galaxy/database/tmp/tmpNoiZ9V -[2016-05-23 08:57:23,648] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 08:57:23,650] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:57:23,652] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:57:23,653] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:57:23,678] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:57:23,706] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:57:23,712] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',) -[2016-05-23 08:57:23,719] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 08:57:23,726] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:57:23,733] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:57:23,735] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:57:23,737] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('multiqc_WDir',) -[2016-05-23 08:57:23,739] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('multiqc_WDir',) -[2016-05-23 08:57:23,741] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:57:23,742] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:57:23,749] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:57:23,756] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:57:23,762] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:57:23,769] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('multiqc_WDir',) -[2016-05-23 08:57:23,776] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 08:57:23,777] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:57:23,842] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports -[2016-05-23 08:57:23,846] multiqc [INFO ] Report : multiqc_report.html -[2016-05-23 08:57:23,846] multiqc [INFO ] Data : multiqc_data -[2016-05-23 08:57:23,846] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpNoiZ9V/multiqc_data/multiqc_fastqc.txt' to '/root/galaxy/database/jobs_directory/000/88/working/multiqc_data' -[2016-05-23 08:57:23,846] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpNoiZ9V/multiqc_data/multiqc_general_stats.txt' to '/root/galaxy/database/jobs_directory/000/88/working/multiqc_data' -[2016-05-23 08:57:23,846] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpNoiZ9V/multiqc_data/multiqc_sources.txt' to '/root/galaxy/database/jobs_directory/000/88/working/multiqc_data' -[2016-05-23 08:57:23,919] multiqc [INFO ] MultiQC complete |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/log_featurecounts.txt --- a/test-data/log_featurecounts.txt Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,38 +0,0 @@ -[2016-05-23 08:51:46,431] multiqc [INFO ] This is MultiQC v0.6 -[2016-05-23 08:51:46,431] multiqc [DEBUG ] Command : /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/bin/multiqc multiqc_WDir -[2016-05-23 08:51:46,431] multiqc [DEBUG ] Working dir : /root/galaxy/database/jobs_directory/000/86/working -[2016-05-23 08:51:46,431] multiqc [DEBUG ] Template : default -[2016-05-23 08:51:46,431] multiqc [DEBUG ] No MultiQC config found: /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/lib/python/multiqc-0.6-py2.7.egg/multiqc_config.yaml -[2016-05-23 08:51:46,431] multiqc [DEBUG ] No MultiQC config found: /root/.multiqc_config.yaml -[2016-05-23 08:51:46,432] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml -[2016-05-23 08:51:46,492] multiqc [INFO ] Searching 'multiqc_WDir' -[2016-05-23 08:51:46,492] multiqc [DEBUG ] Analysing modules: snpeff, qualimap, featureCounts, methylQA, rseqc, picard, preseq, samblaster, samtools, bamtools, bismark, hicup, salmon, star, tophat, bowtie2, bowtie1, cutadapt, trimmomatic, skewer, fastq_screen, fastqc -[2016-05-23 08:51:46,492] multiqc [DEBUG ] Using temporary directory for creating report: /root/galaxy/database/tmp/tmpl8m33T -[2016-05-23 08:51:46,498] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 08:51:46,500] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:51:46,502] multiqc.modules.featureCounts.feature_counts [INFO ] Found 6 reports -[2016-05-23 08:51:46,505] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:51:46,508] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:51:46,510] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:51:46,512] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',) -[2016-05-23 08:51:46,513] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 08:51:46,515] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:51:46,516] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:51:46,519] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:51:46,520] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('multiqc_WDir',) -[2016-05-23 08:51:46,522] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('multiqc_WDir',) -[2016-05-23 08:51:46,524] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:51:46,526] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:51:46,527] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:51:46,529] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:51:46,531] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:51:46,532] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('multiqc_WDir',) -[2016-05-23 08:51:46,534] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 08:51:46,535] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:51:46,537] multiqc.modules.fastqc.fastqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:51:46,538] multiqc [INFO ] Report : multiqc_report.html -[2016-05-23 08:51:46,538] multiqc [INFO ] Data : multiqc_data -[2016-05-23 08:51:46,538] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpl8m33T/multiqc_data/multiqc_general_stats.txt' to '/root/galaxy/database/jobs_directory/000/86/working/multiqc_data' -[2016-05-23 08:51:46,539] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpl8m33T/multiqc_data/multiqc_sources.txt' to '/root/galaxy/database/jobs_directory/000/86/working/multiqc_data' -[2016-05-23 08:51:46,539] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpl8m33T/multiqc_data/multiqc_featureCounts.txt' to '/root/galaxy/database/jobs_directory/000/86/working/multiqc_data' -[2016-05-23 08:51:46,610] multiqc [INFO ] MultiQC complete |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/log_picard.txt --- a/test-data/log_picard.txt Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,41 +0,0 @@ -[2016-05-23 09:33:33,915] multiqc [INFO ] This is MultiQC v0.6 -[2016-05-23 09:33:33,915] multiqc [DEBUG ] Command : /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/bin/multiqc multiqc_WDir -[2016-05-23 09:33:33,916] multiqc [DEBUG ] Working dir : /root/galaxy/database/jobs_directory/000/97/working -[2016-05-23 09:33:33,916] multiqc [DEBUG ] Template : default -[2016-05-23 09:33:33,916] multiqc [DEBUG ] No MultiQC config found: /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/lib/python/multiqc-0.6-py2.7.egg/multiqc_config.yaml -[2016-05-23 09:33:33,916] multiqc [DEBUG ] No MultiQC config found: /root/.multiqc_config.yaml -[2016-05-23 09:33:33,916] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml -[2016-05-23 09:33:34,048] multiqc [INFO ] Searching 'multiqc_WDir' -[2016-05-23 09:33:34,049] multiqc [DEBUG ] Analysing modules: snpeff, qualimap, featureCounts, methylQA, rseqc, picard, preseq, samblaster, samtools, bamtools, bismark, hicup, salmon, star, tophat, bowtie2, bowtie1, cutadapt, trimmomatic, skewer, fastq_screen, fastqc -[2016-05-23 09:33:34,049] multiqc [DEBUG ] Using temporary directory for creating report: /root/galaxy/database/tmp/tmp4Zyt3V -[2016-05-23 09:33:34,056] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 09:33:34,057] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:33:34,059] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:33:34,061] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:33:34,069] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:33:34,083] multiqc.modules.picard.picard [INFO ] Found 1 dupMetrics reports -[2016-05-23 09:33:34,083] multiqc.modules.picard.picard [INFO ] Found 1 insertSize reports -[2016-05-23 09:33:34,088] multiqc.modules.picard.picard [INFO ] Found 1 GCbias reports -[2016-05-23 09:33:34,091] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',) -[2016-05-23 09:33:34,094] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 09:33:34,097] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:33:34,100] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:33:34,102] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:33:34,104] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('multiqc_WDir',) -[2016-05-23 09:33:34,106] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('multiqc_WDir',) -[2016-05-23 09:33:34,108] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:33:34,110] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:33:34,113] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:33:34,116] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:33:34,118] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:33:34,121] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('multiqc_WDir',) -[2016-05-23 09:33:34,124] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 09:33:34,126] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:33:34,128] multiqc.modules.fastqc.fastqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:33:34,129] multiqc [INFO ] Report : multiqc_report.html -[2016-05-23 09:33:34,129] multiqc [INFO ] Data : multiqc_data -[2016-05-23 09:33:34,130] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmp4Zyt3V/multiqc_data/multiqc_picard_dups.txt' to '/root/galaxy/database/jobs_directory/000/97/working/multiqc_data' -[2016-05-23 09:33:34,130] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmp4Zyt3V/multiqc_data/multiqc_general_stats.txt' to '/root/galaxy/database/jobs_directory/000/97/working/multiqc_data' -[2016-05-23 09:33:34,130] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmp4Zyt3V/multiqc_data/multiqc_picard_insertSize.txt' to '/root/galaxy/database/jobs_directory/000/97/working/multiqc_data' -[2016-05-23 09:33:34,130] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmp4Zyt3V/multiqc_data/multiqc_sources.txt' to '/root/galaxy/database/jobs_directory/000/97/working/multiqc_data' -[2016-05-23 09:33:34,206] multiqc [INFO ] MultiQC complete |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/log_samtools.txt --- a/test-data/log_samtools.txt Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,38 +0,0 @@ -[2016-05-23 09:14:29,851] multiqc [INFO ] This is MultiQC v0.6 -[2016-05-23 09:14:29,851] multiqc [DEBUG ] Command : /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/bin/multiqc multiqc_WDir -[2016-05-23 09:14:29,851] multiqc [DEBUG ] Working dir : /root/galaxy/database/jobs_directory/000/89/working -[2016-05-23 09:14:29,851] multiqc [DEBUG ] Template : default -[2016-05-23 09:14:29,851] multiqc [DEBUG ] No MultiQC config found: /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/lib/python/multiqc-0.6-py2.7.egg/multiqc_config.yaml -[2016-05-23 09:14:29,851] multiqc [DEBUG ] No MultiQC config found: /root/.multiqc_config.yaml -[2016-05-23 09:14:29,851] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml -[2016-05-23 09:14:29,979] multiqc [INFO ] Searching 'multiqc_WDir' -[2016-05-23 09:14:29,979] multiqc [DEBUG ] Analysing modules: snpeff, qualimap, featureCounts, methylQA, rseqc, picard, preseq, samblaster, samtools, bamtools, bismark, hicup, salmon, star, tophat, bowtie2, bowtie1, cutadapt, trimmomatic, skewer, fastq_screen, fastqc -[2016-05-23 09:14:29,979] multiqc [DEBUG ] Using temporary directory for creating report: /root/galaxy/database/tmp/tmpbM5r93 -[2016-05-23 09:14:29,986] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 09:14:29,988] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:14:29,989] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:14:29,991] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:14:30,048] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:14:30,107] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:14:30,120] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',) -[2016-05-23 09:14:30,132] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 09:14:30,157] multiqc.modules.samtools.samtools [INFO ] Found 1 reports -[2016-05-23 09:14:30,170] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:14:30,173] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:14:30,175] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('multiqc_WDir',) -[2016-05-23 09:14:30,177] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('multiqc_WDir',) -[2016-05-23 09:14:30,178] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:14:30,180] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:14:30,193] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:14:30,205] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:14:30,218] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:14:30,230] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('multiqc_WDir',) -[2016-05-23 09:14:30,242] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 09:14:30,244] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:14:30,246] multiqc.modules.fastqc.fastqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 09:14:30,247] multiqc [INFO ] Report : multiqc_report.html -[2016-05-23 09:14:30,247] multiqc [INFO ] Data : multiqc_data -[2016-05-23 09:14:30,247] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpbM5r93/multiqc_data/multiqc_general_stats.txt' to '/root/galaxy/database/jobs_directory/000/89/working/multiqc_data' -[2016-05-23 09:14:30,247] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpbM5r93/multiqc_data/multiqc_samtools.txt' to '/root/galaxy/database/jobs_directory/000/89/working/multiqc_data' -[2016-05-23 09:14:30,247] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpbM5r93/multiqc_data/multiqc_sources.txt' to '/root/galaxy/database/jobs_directory/000/89/working/multiqc_data' -[2016-05-23 09:14:30,322] multiqc [INFO ] MultiQC complete |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/log_tophat.txt --- a/test-data/log_tophat.txt Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,38 +0,0 @@ -[2016-05-23 08:46:00,804] multiqc [INFO ] This is MultiQC v0.6 -[2016-05-23 08:46:00,804] multiqc [DEBUG ] Command : /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/bin/multiqc multiqc_WDir -[2016-05-23 08:46:00,804] multiqc [DEBUG ] Working dir : /root/galaxy/database/jobs_directory/000/85/working -[2016-05-23 08:46:00,804] multiqc [DEBUG ] Template : default -[2016-05-23 08:46:00,804] multiqc [DEBUG ] No MultiQC config found: /root/dependencies/multiqc/0.6/cmonjeau/package_multiqc_0_6/021c59fc29be/lib/python/multiqc-0.6-py2.7.egg/multiqc_config.yaml -[2016-05-23 08:46:00,804] multiqc [DEBUG ] No MultiQC config found: /root/.multiqc_config.yaml -[2016-05-23 08:46:00,804] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml -[2016-05-23 08:46:00,928] multiqc [INFO ] Searching 'multiqc_WDir' -[2016-05-23 08:46:00,928] multiqc [DEBUG ] Analysing modules: snpeff, qualimap, featureCounts, methylQA, rseqc, picard, preseq, samblaster, samtools, bamtools, bismark, hicup, salmon, star, tophat, bowtie2, bowtie1, cutadapt, trimmomatic, skewer, fastq_screen, fastqc -[2016-05-23 08:46:00,928] multiqc [DEBUG ] Using temporary directory for creating report: /root/galaxy/database/tmp/tmpTu_Bvi -[2016-05-23 08:46:00,935] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 08:46:00,937] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:46:00,939] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:46:00,940] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:46:00,944] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:46:00,946] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:46:00,948] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',) -[2016-05-23 08:46:00,950] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 08:46:00,951] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:46:00,953] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:46:00,956] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:46:00,957] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('multiqc_WDir',) -[2016-05-23 08:46:00,959] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('multiqc_WDir',) -[2016-05-23 08:46:00,961] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:46:00,964] multiqc.modules.tophat.tophat [INFO ] Found 1 reports -[2016-05-23 08:46:00,966] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:46:00,968] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:46:00,970] multiqc.modules.cutadapt.cutadapt [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:46:00,971] multiqc.modules.trimmomatic.trimmomatic [DEBUG ] Could not find any Trimmomatic data in ('multiqc_WDir',) -[2016-05-23 08:46:00,973] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('multiqc_WDir',) -[2016-05-23 08:46:00,975] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:46:00,977] multiqc.modules.fastqc.fastqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) -[2016-05-23 08:46:00,977] multiqc [INFO ] Report : multiqc_report.html -[2016-05-23 08:46:00,978] multiqc [INFO ] Data : multiqc_data -[2016-05-23 08:46:00,978] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpTu_Bvi/multiqc_data/multiqc_general_stats.txt' to '/root/galaxy/database/jobs_directory/000/85/working/multiqc_data' -[2016-05-23 08:46:00,978] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpTu_Bvi/multiqc_data/multiqc_sources.txt' to '/root/galaxy/database/jobs_directory/000/85/working/multiqc_data' -[2016-05-23 08:46:00,978] multiqc [DEBUG ] Moving data file from '/root/galaxy/database/tmp/tmpTu_Bvi/multiqc_data/multiqc_tophat.txt.txt' to '/root/galaxy/database/jobs_directory/000/85/working/multiqc_data' -[2016-05-23 08:46:01,051] multiqc [INFO ] MultiQC complete |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/report_all.html --- a/test-data/report_all.html Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,4440 +0,0 @@\n-<!DOCTYPE html>\n-<html lang="en">\n-<head>\n- \n- \n-\n-<meta charset="utf-8">\n-<meta http-equiv="X-UA-Compatible" content="IE=edge">\n-<meta name="viewport" content="width=device-width, initial-scale=1">\n-\n-<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n-<meta name="author" content="MultiQC">\n-<title>MultiQC Report</title>\n-\n-<!-- early variable initialisation -->\n-<script type="text/javascript">mqc_plots = {}; num_datasets_plot_limit = 50;</script>\n- \n- \n-\n-<!-- Favicon includes -->\n-<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,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">\n-<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,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'..b'HZC5D95fQRlgqDCd9PssvDD8aS7JwmmqHimkXQCSKTlZ6DzG+OrlIOg5An9rwc8YVDIBkMjuE7RPY0Kj9DTgcdXzRny85gC99vstOxRymPxjOY8N0kexZpR0NZQPnlc15Uw2DCdxtbuOdx9OPgTnl4hDz2a8muO8MH/xdgAF+gE91daYKQAAAAAElFTkSuQmCC" style="height:41px;">\n- </a>\n- <strong>\n- <a href="http://multiqc.info" target="_blank">MultiQC v0.6</a>\n- </strong>\n- - Written by <a href="http://phil.ewels.co.uk" target="_blank">Phil Ewels</a>,\n- available on <a href="https://github.com/ewels/MultiQC" target="_blank">GitHub</a>.\n-</p>\n-<p>\n- This report uses <a href="http://www.highcharts.com/" target="_blank">HighCharts</a>,\n- <a href="https://jquery.com/" target="_blank">jQuery</a>,\n- <a href="http://getbootstrap.com/" target="_blank">Bootstrap</a>,\n- <a href="https://github.com/gka/chroma.js" target="_blank">chroma.js</a>\n- and <a href="http://bootstraptour.com/" target="_blank">Bootstrap Tour</a>.\n-</p>\n- </div>\n-</div>\n-\n-\n-\n-\n-<!-- Regex Help Modal -->\n-<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n- <div class="modal-dialog" role="document">\n- <div class="modal-content">\n- <div class="modal-header">\n- <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n- <h3 class="modal-title">Regex Help</h3>\n- </div>\n- <div class="modal-body">\n- <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n- <div class="row">\n- <div class="col-sm-6 regex_example_buttons">\n- <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n- <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n- <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n- <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n- <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n- <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n- <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n- <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n- <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n- <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n- <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n- <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n- <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n- </div>\n- <div class="col-sm-6 regex_example_demo">\n- <input type="text" class="form-control" />\n-<pre>\n-<span>samp_1</span>\n-<span>samp_1_edited</span>\n-<span>samp_2</span>\n-<span>samp_2_edited</span>\n-<span>samp_3</span>\n-<span>samp_3_edited</span>\n-<span>prepended_samp_1</span>\n-<span>tmp_samp_1_edited</span>\n-<span>tmpp_samp_1_edited</span>\n-<span>tmppp_samp_1_edited</span>\n-<span>#samp_1_edited.tmp</span>\n-<span>samp_11</span>\n-<span>samp_11111</span>\n-</pre>\n- <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n- </div>\n- </div>\n- </div>\n- <div class="modal-footer">\n- <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n- </div>\n- </div>\n- </div>\n-</div>\n-\n-</body>\n-</html>\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/report_bismark.html --- a/test-data/report_bismark.html Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,3437 +0,0 @@\n-<!DOCTYPE html>\n-<html lang="en">\n-<head>\n- \n- \n-\n-<meta charset="utf-8">\n-<meta http-equiv="X-UA-Compatible" content="IE=edge">\n-<meta name="viewport" content="width=device-width, initial-scale=1">\n-\n-<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n-<meta name="author" content="MultiQC">\n-<title>MultiQC Report</title>\n-\n-<!-- early variable initialisation -->\n-<script type="text/javascript">mqc_plots = {}; num_datasets_plot_limit = 50;</script>\n- \n- \n-\n-<!-- Favicon includes -->\n-<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,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">\n-<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,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'..b'HZC5D95fQRlgqDCd9PssvDD8aS7JwmmqHimkXQCSKTlZ6DzG+OrlIOg5An9rwc8YVDIBkMjuE7RPY0Kj9DTgcdXzRny85gC99vstOxRymPxjOY8N0kexZpR0NZQPnlc15Uw2DCdxtbuOdx9OPgTnl4hDz2a8muO8MH/xdgAF+gE91daYKQAAAAAElFTkSuQmCC" style="height:41px;">\n- </a>\n- <strong>\n- <a href="http://multiqc.info" target="_blank">MultiQC v0.6</a>\n- </strong>\n- - Written by <a href="http://phil.ewels.co.uk" target="_blank">Phil Ewels</a>,\n- available on <a href="https://github.com/ewels/MultiQC" target="_blank">GitHub</a>.\n-</p>\n-<p>\n- This report uses <a href="http://www.highcharts.com/" target="_blank">HighCharts</a>,\n- <a href="https://jquery.com/" target="_blank">jQuery</a>,\n- <a href="http://getbootstrap.com/" target="_blank">Bootstrap</a>,\n- <a href="https://github.com/gka/chroma.js" target="_blank">chroma.js</a>\n- and <a href="http://bootstraptour.com/" target="_blank">Bootstrap Tour</a>.\n-</p>\n- </div>\n-</div>\n-\n-\n-\n-\n-<!-- Regex Help Modal -->\n-<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n- <div class="modal-dialog" role="document">\n- <div class="modal-content">\n- <div class="modal-header">\n- <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n- <h3 class="modal-title">Regex Help</h3>\n- </div>\n- <div class="modal-body">\n- <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n- <div class="row">\n- <div class="col-sm-6 regex_example_buttons">\n- <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n- <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n- <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n- <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n- <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n- <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n- <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n- <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n- <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n- <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n- <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n- <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n- <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n- </div>\n- <div class="col-sm-6 regex_example_demo">\n- <input type="text" class="form-control" />\n-<pre>\n-<span>samp_1</span>\n-<span>samp_1_edited</span>\n-<span>samp_2</span>\n-<span>samp_2_edited</span>\n-<span>samp_3</span>\n-<span>samp_3_edited</span>\n-<span>prepended_samp_1</span>\n-<span>tmp_samp_1_edited</span>\n-<span>tmpp_samp_1_edited</span>\n-<span>tmppp_samp_1_edited</span>\n-<span>#samp_1_edited.tmp</span>\n-<span>samp_11</span>\n-<span>samp_11111</span>\n-</pre>\n- <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n- </div>\n- </div>\n- </div>\n- <div class="modal-footer">\n- <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n- </div>\n- </div>\n- </div>\n-</div>\n-\n-</body>\n-</html>\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/report_cutadapt.html --- a/test-data/report_cutadapt.html Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,3393 +0,0 @@\n-<!DOCTYPE html>\n-<html lang="en">\n-<head>\n- \n- \n-\n-<meta charset="utf-8">\n-<meta http-equiv="X-UA-Compatible" content="IE=edge">\n-<meta name="viewport" content="width=device-width, initial-scale=1">\n-\n-<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n-<meta name="author" content="MultiQC">\n-<title>MultiQC Report</title>\n-\n-<!-- early variable initialisation -->\n-<script type="text/javascript">mqc_plots = {}; num_datasets_plot_limit = 50;</script>\n- \n- \n-\n-<!-- Favicon includes -->\n-<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACAAAAAgCAMAAABEpIrGAAAABGdBTUEAALGPC/xhBQAAAAFzUkdCAK7OHOkAAAAgY0hSTQAAeiYAAICEAAD6AAAAgOgAAHUwAADqYAAAOpgAABdwnLpRPAAAAgRQTFRFAAAAHR0bvhYi0QkfuRojAJZAAJY/IWzIHnC9HXG4HR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bvhYivhYivhYivhYivhYivhYivhYiwBUiwRQhwRQhwxIh3gEdyBAgQGs2KHs6KXo6KXo5JX06BZI/AJhAAJdAAJdAAJc/AJc+AJc+AJc+AJc8AJ0pBo9XFHyUFnqbFnqaGXemHXG5H2/AHXG5HXG5HXG5HXG4HXG4HXG4HXG4HXG4HXG4HXG4HR0b////FByqhAAAAKp0Uk5TAAAAAAAAAAAAAAESGBcRBgoJnNPQ0rQcWVoLwPtXAqFuv5Mk3NoibP79XQSo+vSbAyzj9+7H4Cl18s7wifFjB7C9nryjBTTpdJFQgOYvfe04Nexot6yXYrKrPeo2heIromkq4ZlrpbFRtW1k/MjUHbuY9ktSw8R673h3M2ETOj08FhiRvLi6aAIJMEtKSkkzBzyxurm6sTkBEj1JSUEeAmq9vL6UHQcWFwlLDobJAAAAAWJLR0SryQFnKAAAAAlwSFlzAAAuIwAALiMBeKU/dgAAAa5JREFUOMut0tdXE0EYBfD9QBRIIgkEDZDQhUBQAgGlBCIlSlGqSlFBVKoiSu8oHQWpIhaUpuD9K50JOXlgJm/cp2/u+Z3dnZ1RFApUqTUa9eVAUk5DQRoWtdaz1gWH6PWhV656CoOeJTTMsw6PAIvR5C4oMoqvEe0B2hhXEet+B8XFy8G1BDdINMtBUrKrIUsKJOD6DSDVyitKS4fZZj4LMjKBm7dcIAvIzhGekGvPgzmfVeS4DRQUCsBmKgKKnaTQnbtASakAjGXlwL37RFQBVFbFCiDJUF0D1BJpHwAPHY/EbdZZ6oEGBzVmcJcqglr+9Y+f0FOgqZmeiaCFnr9gZTibX1qtDSJoJWsb0N6RDaOBHJ0i6CJ69RqV3cCbHtK9lYKeEID9YjuRrkgK6B0/o94+b0ChfhsbBlTegWqQDUMkANeV44DswHAjG84Ap2FkdHSMn2Rz1sg4u8xkMbmb88nE5JSXvP/g48PA9MzsnDzzC4u+DFxY+vhpWZqVz6trfkz4rW9sbknzZfvrRQ52vn3/Ic/P3V+XmPD/vbd/IM/h0R++kYC/x95y8u8/kOgi2/X4mGIAAAAldEVYdGRhdGU6Y3JlYXRlADIwMTYtMDQtMTlUMDk6MjM6NDErMDA6MDCtzsBUAAAAJXRFWHRkYXRlOm1vZGlmeQAyMDE2LTA0LTE5VDA5OjIzOjQxKzAwOjAw3JN46AAAAEZ0RVh0c29mdHdhcmUASW1hZ2VNYWdpY2sgNi43LjgtOSAyMDE0LTA1LTEyIFExNiBodHRwOi8vd3d3LmltYWdlbWFnaWNrLm9yZ9yG7QAAAAAYdEVYdFRodW1iOjpEb2N1bWVudDo6UGFnZXMAMaf/uy8AAAAYdEVYdFRodW1iOjpJbWFnZTo6aGVpZ2h0ADE5Mg8AcoUAAAAXdEVYdFRodW1iOjpJbWFnZTo6V2lkdGgAMTky06whCAAAABl0RVh0VGh1bWI6Ok1pbWV0eXBlAGltYWdlL3BuZz+yVk4AAAAXdEVYdFRodW1iOjpNVGltZQAxNDYxMDU3ODIxUvThswAAAA90RVh0VGh1bWI6OlNpemUAMEJClKI+7AAAAFZ0RVh0VGh1bWI6OlVSSQBmaWxlOi8vL21udGxvZy9mYXZpY29ucy8yMDE2LTA0LTE5L2Y2MDUzNWMzMThlMzdlYmRhNzJkZTJlNTJhNWJiNzk5Lmljby5wbme1EtGEAAAAAElFTkSuQmCC">\n-<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,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'..b'HZC5D95fQRlgqDCd9PssvDD8aS7JwmmqHimkXQCSKTlZ6DzG+OrlIOg5An9rwc8YVDIBkMjuE7RPY0Kj9DTgcdXzRny85gC99vstOxRymPxjOY8N0kexZpR0NZQPnlc15Uw2DCdxtbuOdx9OPgTnl4hDz2a8muO8MH/xdgAF+gE91daYKQAAAAAElFTkSuQmCC" style="height:41px;">\n- </a>\n- <strong>\n- <a href="http://multiqc.info" target="_blank">MultiQC v0.6</a>\n- </strong>\n- - Written by <a href="http://phil.ewels.co.uk" target="_blank">Phil Ewels</a>,\n- available on <a href="https://github.com/ewels/MultiQC" target="_blank">GitHub</a>.\n-</p>\n-<p>\n- This report uses <a href="http://www.highcharts.com/" target="_blank">HighCharts</a>,\n- <a href="https://jquery.com/" target="_blank">jQuery</a>,\n- <a href="http://getbootstrap.com/" target="_blank">Bootstrap</a>,\n- <a href="https://github.com/gka/chroma.js" target="_blank">chroma.js</a>\n- and <a href="http://bootstraptour.com/" target="_blank">Bootstrap Tour</a>.\n-</p>\n- </div>\n-</div>\n-\n-\n-\n-\n-<!-- Regex Help Modal -->\n-<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n- <div class="modal-dialog" role="document">\n- <div class="modal-content">\n- <div class="modal-header">\n- <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n- <h3 class="modal-title">Regex Help</h3>\n- </div>\n- <div class="modal-body">\n- <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n- <div class="row">\n- <div class="col-sm-6 regex_example_buttons">\n- <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n- <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n- <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n- <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n- <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n- <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n- <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n- <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n- <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n- <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n- <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n- <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n- <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n- </div>\n- <div class="col-sm-6 regex_example_demo">\n- <input type="text" class="form-control" />\n-<pre>\n-<span>samp_1</span>\n-<span>samp_1_edited</span>\n-<span>samp_2</span>\n-<span>samp_2_edited</span>\n-<span>samp_3</span>\n-<span>samp_3_edited</span>\n-<span>prepended_samp_1</span>\n-<span>tmp_samp_1_edited</span>\n-<span>tmpp_samp_1_edited</span>\n-<span>tmppp_samp_1_edited</span>\n-<span>#samp_1_edited.tmp</span>\n-<span>samp_11</span>\n-<span>samp_11111</span>\n-</pre>\n- <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n- </div>\n- </div>\n- </div>\n- <div class="modal-footer">\n- <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n- </div>\n- </div>\n- </div>\n-</div>\n-\n-</body>\n-</html>\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/report_fastqc.html --- a/test-data/report_fastqc.html Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,3950 +0,0 @@\n-<!DOCTYPE html>\n-<html lang="en">\n-<head>\n- \n- \n-\n-<meta charset="utf-8">\n-<meta http-equiv="X-UA-Compatible" content="IE=edge">\n-<meta name="viewport" content="width=device-width, initial-scale=1">\n-\n-<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n-<meta name="author" content="MultiQC">\n-<title>MultiQC Report</title>\n-\n-<!-- early variable initialisation -->\n-<script type="text/javascript">mqc_plots = {}; num_datasets_plot_limit = 50;</script>\n- \n- \n-\n-<!-- Favicon includes -->\n-<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAACAAAAAgCAMAAABEpIrGAAAABGdBTUEAALGPC/xhBQAAAAFzUkdCAK7OHOkAAAAgY0hSTQAAeiYAAICEAAD6AAAAgOgAAHUwAADqYAAAOpgAABdwnLpRPAAAAgRQTFRFAAAAHR0bvhYi0QkfuRojAJZAAJY/IWzIHnC9HXG4HR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bHR0bvhYivhYivhYivhYivhYivhYivhYiwBUiwRQhwRQhwxIh3gEdyBAgQGs2KHs6KXo6KXo5JX06BZI/AJhAAJdAAJdAAJc/AJc+AJc+AJc+AJc8AJ0pBo9XFHyUFnqbFnqaGXemHXG5H2/AHXG5HXG5HXG5HXG4HXG4HXG4HXG4HXG4HXG4HXG4HR0b////FByqhAAAAKp0Uk5TAAAAAAAAAAAAAAESGBcRBgoJnNPQ0rQcWVoLwPtXAqFuv5Mk3NoibP79XQSo+vSbAyzj9+7H4Cl18s7wifFjB7C9nryjBTTpdJFQgOYvfe04Nexot6yXYrKrPeo2heIromkq4ZlrpbFRtW1k/MjUHbuY9ktSw8R673h3M2ETOj08FhiRvLi6aAIJMEtKSkkzBzyxurm6sTkBEj1JSUEeAmq9vL6UHQcWFwlLDobJAAAAAWJLR0SryQFnKAAAAAlwSFlzAAAuIwAALiMBeKU/dgAAAa5JREFUOMut0tdXE0EYBfD9QBRIIgkEDZDQhUBQAgGlBCIlSlGqSlFBVKoiSu8oHQWpIhaUpuD9K50JOXlgJm/cp2/u+Z3dnZ1RFApUqTUa9eVAUk5DQRoWtdaz1gWH6PWhV656CoOeJTTMsw6PAIvR5C4oMoqvEe0B2hhXEet+B8XFy8G1BDdINMtBUrKrIUsKJOD6DSDVyitKS4fZZj4LMjKBm7dcIAvIzhGekGvPgzmfVeS4DRQUCsBmKgKKnaTQnbtASakAjGXlwL37RFQBVFbFCiDJUF0D1BJpHwAPHY/EbdZZ6oEGBzVmcJcqglr+9Y+f0FOgqZmeiaCFnr9gZTibX1qtDSJoJWsb0N6RDaOBHJ0i6CJ69RqV3cCbHtK9lYKeEID9YjuRrkgK6B0/o94+b0ChfhsbBlTegWqQDUMkANeV44DswHAjG84Ap2FkdHSMn2Rz1sg4u8xkMbmb88nE5JSXvP/g48PA9MzsnDzzC4u+DFxY+vhpWZqVz6trfkz4rW9sbknzZfvrRQ52vn3/Ic/P3V+XmPD/vbd/IM/h0R++kYC/x95y8u8/kOgi2/X4mGIAAAAldEVYdGRhdGU6Y3JlYXRlADIwMTYtMDQtMTlUMDk6MjM6NDErMDA6MDCtzsBUAAAAJXRFWHRkYXRlOm1vZGlmeQAyMDE2LTA0LTE5VDA5OjIzOjQxKzAwOjAw3JN46AAAAEZ0RVh0c29mdHdhcmUASW1hZ2VNYWdpY2sgNi43LjgtOSAyMDE0LTA1LTEyIFExNiBodHRwOi8vd3d3LmltYWdlbWFnaWNrLm9yZ9yG7QAAAAAYdEVYdFRodW1iOjpEb2N1bWVudDo6UGFnZXMAMaf/uy8AAAAYdEVYdFRodW1iOjpJbWFnZTo6aGVpZ2h0ADE5Mg8AcoUAAAAXdEVYdFRodW1iOjpJbWFnZTo6V2lkdGgAMTky06whCAAAABl0RVh0VGh1bWI6Ok1pbWV0eXBlAGltYWdlL3BuZz+yVk4AAAAXdEVYdFRodW1iOjpNVGltZQAxNDYxMDU3ODIxUvThswAAAA90RVh0VGh1bWI6OlNpemUAMEJClKI+7AAAAFZ0RVh0VGh1bWI6OlVSSQBmaWxlOi8vL21udGxvZy9mYXZpY29ucy8yMDE2LTA0LTE5L2Y2MDUzNWMzMThlMzdlYmRhNzJkZTJlNTJhNWJiNzk5Lmljby5wbme1EtGEAAAAAElFTkSuQmCC">\n-<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,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'..b'HZC5D95fQRlgqDCd9PssvDD8aS7JwmmqHimkXQCSKTlZ6DzG+OrlIOg5An9rwc8YVDIBkMjuE7RPY0Kj9DTgcdXzRny85gC99vstOxRymPxjOY8N0kexZpR0NZQPnlc15Uw2DCdxtbuOdx9OPgTnl4hDz2a8muO8MH/xdgAF+gE91daYKQAAAAAElFTkSuQmCC" style="height:41px;">\n- </a>\n- <strong>\n- <a href="http://multiqc.info" target="_blank">MultiQC v0.6</a>\n- </strong>\n- - Written by <a href="http://phil.ewels.co.uk" target="_blank">Phil Ewels</a>,\n- available on <a href="https://github.com/ewels/MultiQC" target="_blank">GitHub</a>.\n-</p>\n-<p>\n- This report uses <a href="http://www.highcharts.com/" target="_blank">HighCharts</a>,\n- <a href="https://jquery.com/" target="_blank">jQuery</a>,\n- <a href="http://getbootstrap.com/" target="_blank">Bootstrap</a>,\n- <a href="https://github.com/gka/chroma.js" target="_blank">chroma.js</a>\n- and <a href="http://bootstraptour.com/" target="_blank">Bootstrap Tour</a>.\n-</p>\n- </div>\n-</div>\n-\n-\n-\n-\n-<!-- Regex Help Modal -->\n-<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n- <div class="modal-dialog" role="document">\n- <div class="modal-content">\n- <div class="modal-header">\n- <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n- <h3 class="modal-title">Regex Help</h3>\n- </div>\n- <div class="modal-body">\n- <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n- <div class="row">\n- <div class="col-sm-6 regex_example_buttons">\n- <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n- <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n- <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n- <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n- <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n- <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n- <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n- <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n- <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n- <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n- <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n- <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n- <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n- </div>\n- <div class="col-sm-6 regex_example_demo">\n- <input type="text" class="form-control" />\n-<pre>\n-<span>samp_1</span>\n-<span>samp_1_edited</span>\n-<span>samp_2</span>\n-<span>samp_2_edited</span>\n-<span>samp_3</span>\n-<span>samp_3_edited</span>\n-<span>prepended_samp_1</span>\n-<span>tmp_samp_1_edited</span>\n-<span>tmpp_samp_1_edited</span>\n-<span>tmppp_samp_1_edited</span>\n-<span>#samp_1_edited.tmp</span>\n-<span>samp_11</span>\n-<span>samp_11111</span>\n-</pre>\n- <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n- </div>\n- </div>\n- </div>\n- <div class="modal-footer">\n- <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n- </div>\n- </div>\n- </div>\n-</div>\n-\n-</body>\n-</html>\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/report_fastqc_2.html --- a/test-data/report_fastqc_2.html Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,3950 +0,0 @@\n-<!DOCTYPE html>\n-<html lang="en">\n-<head>\n- \n- \n-\n-<meta charset="utf-8">\n-<meta http-equiv="X-UA-Compatible" content="IE=edge">\n-<meta name="viewport" content="width=device-width, initial-scale=1">\n-\n-<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n-<meta name="author" content="MultiQC">\n-<title>MultiQC Report</title>\n-\n-<!-- early variable initialisation -->\n-<script type="text/javascript">mqc_plots = {}; num_datasets_plot_limit = 50;</script>\n- \n- \n-\n-<!-- Favicon includes -->\n-<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,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">\n-<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,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'..b'HZC5D95fQRlgqDCd9PssvDD8aS7JwmmqHimkXQCSKTlZ6DzG+OrlIOg5An9rwc8YVDIBkMjuE7RPY0Kj9DTgcdXzRny85gC99vstOxRymPxjOY8N0kexZpR0NZQPnlc15Uw2DCdxtbuOdx9OPgTnl4hDz2a8muO8MH/xdgAF+gE91daYKQAAAAAElFTkSuQmCC" style="height:41px;">\n- </a>\n- <strong>\n- <a href="http://multiqc.info" target="_blank">MultiQC v0.6</a>\n- </strong>\n- - Written by <a href="http://phil.ewels.co.uk" target="_blank">Phil Ewels</a>,\n- available on <a href="https://github.com/ewels/MultiQC" target="_blank">GitHub</a>.\n-</p>\n-<p>\n- This report uses <a href="http://www.highcharts.com/" target="_blank">HighCharts</a>,\n- <a href="https://jquery.com/" target="_blank">jQuery</a>,\n- <a href="http://getbootstrap.com/" target="_blank">Bootstrap</a>,\n- <a href="https://github.com/gka/chroma.js" target="_blank">chroma.js</a>\n- and <a href="http://bootstraptour.com/" target="_blank">Bootstrap Tour</a>.\n-</p>\n- </div>\n-</div>\n-\n-\n-\n-\n-<!-- Regex Help Modal -->\n-<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n- <div class="modal-dialog" role="document">\n- <div class="modal-content">\n- <div class="modal-header">\n- <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n- <h3 class="modal-title">Regex Help</h3>\n- </div>\n- <div class="modal-body">\n- <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n- <div class="row">\n- <div class="col-sm-6 regex_example_buttons">\n- <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n- <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n- <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n- <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n- <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n- <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n- <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n- <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n- <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n- <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n- <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n- <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n- <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n- </div>\n- <div class="col-sm-6 regex_example_demo">\n- <input type="text" class="form-control" />\n-<pre>\n-<span>samp_1</span>\n-<span>samp_1_edited</span>\n-<span>samp_2</span>\n-<span>samp_2_edited</span>\n-<span>samp_3</span>\n-<span>samp_3_edited</span>\n-<span>prepended_samp_1</span>\n-<span>tmp_samp_1_edited</span>\n-<span>tmpp_samp_1_edited</span>\n-<span>tmppp_samp_1_edited</span>\n-<span>#samp_1_edited.tmp</span>\n-<span>samp_11</span>\n-<span>samp_11111</span>\n-</pre>\n- <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n- </div>\n- </div>\n- </div>\n- <div class="modal-footer">\n- <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n- </div>\n- </div>\n- </div>\n-</div>\n-\n-</body>\n-</html>\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/report_featurecounts.html --- a/test-data/report_featurecounts.html Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,3409 +0,0 @@\n-<!DOCTYPE html>\n-<html lang="en">\n-<head>\n- \n- \n-\n-<meta charset="utf-8">\n-<meta http-equiv="X-UA-Compatible" content="IE=edge">\n-<meta name="viewport" content="width=device-width, initial-scale=1">\n-\n-<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n-<meta name="author" content="MultiQC">\n-<title>MultiQC Report</title>\n-\n-<!-- early variable initialisation -->\n-<script type="text/javascript">mqc_plots = {}; num_datasets_plot_limit = 50;</script>\n- \n- \n-\n-<!-- Favicon includes -->\n-<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,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">\n-<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,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'..b'HZC5D95fQRlgqDCd9PssvDD8aS7JwmmqHimkXQCSKTlZ6DzG+OrlIOg5An9rwc8YVDIBkMjuE7RPY0Kj9DTgcdXzRny85gC99vstOxRymPxjOY8N0kexZpR0NZQPnlc15Uw2DCdxtbuOdx9OPgTnl4hDz2a8muO8MH/xdgAF+gE91daYKQAAAAAElFTkSuQmCC" style="height:41px;">\n- </a>\n- <strong>\n- <a href="http://multiqc.info" target="_blank">MultiQC v0.6</a>\n- </strong>\n- - Written by <a href="http://phil.ewels.co.uk" target="_blank">Phil Ewels</a>,\n- available on <a href="https://github.com/ewels/MultiQC" target="_blank">GitHub</a>.\n-</p>\n-<p>\n- This report uses <a href="http://www.highcharts.com/" target="_blank">HighCharts</a>,\n- <a href="https://jquery.com/" target="_blank">jQuery</a>,\n- <a href="http://getbootstrap.com/" target="_blank">Bootstrap</a>,\n- <a href="https://github.com/gka/chroma.js" target="_blank">chroma.js</a>\n- and <a href="http://bootstraptour.com/" target="_blank">Bootstrap Tour</a>.\n-</p>\n- </div>\n-</div>\n-\n-\n-\n-\n-<!-- Regex Help Modal -->\n-<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n- <div class="modal-dialog" role="document">\n- <div class="modal-content">\n- <div class="modal-header">\n- <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n- <h3 class="modal-title">Regex Help</h3>\n- </div>\n- <div class="modal-body">\n- <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n- <div class="row">\n- <div class="col-sm-6 regex_example_buttons">\n- <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n- <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n- <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n- <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n- <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n- <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n- <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n- <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n- <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n- <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n- <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n- <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n- <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n- </div>\n- <div class="col-sm-6 regex_example_demo">\n- <input type="text" class="form-control" />\n-<pre>\n-<span>samp_1</span>\n-<span>samp_1_edited</span>\n-<span>samp_2</span>\n-<span>samp_2_edited</span>\n-<span>samp_3</span>\n-<span>samp_3_edited</span>\n-<span>prepended_samp_1</span>\n-<span>tmp_samp_1_edited</span>\n-<span>tmpp_samp_1_edited</span>\n-<span>tmppp_samp_1_edited</span>\n-<span>#samp_1_edited.tmp</span>\n-<span>samp_11</span>\n-<span>samp_11111</span>\n-</pre>\n- <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n- </div>\n- </div>\n- </div>\n- <div class="modal-footer">\n- <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n- </div>\n- </div>\n- </div>\n-</div>\n-\n-</body>\n-</html>\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/report_picard.html --- a/test-data/report_picard.html Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,3482 +0,0 @@\n-<!DOCTYPE html>\n-<html lang="en">\n-<head>\n- \n- \n-\n-<meta charset="utf-8">\n-<meta http-equiv="X-UA-Compatible" content="IE=edge">\n-<meta name="viewport" content="width=device-width, initial-scale=1">\n-\n-<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n-<meta name="author" content="MultiQC">\n-<title>MultiQC Report</title>\n-\n-<!-- early variable initialisation -->\n-<script type="text/javascript">mqc_plots = {}; num_datasets_plot_limit = 50;</script>\n- \n- \n-\n-<!-- Favicon includes -->\n-<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,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">\n-<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,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'..b'HZC5D95fQRlgqDCd9PssvDD8aS7JwmmqHimkXQCSKTlZ6DzG+OrlIOg5An9rwc8YVDIBkMjuE7RPY0Kj9DTgcdXzRny85gC99vstOxRymPxjOY8N0kexZpR0NZQPnlc15Uw2DCdxtbuOdx9OPgTnl4hDz2a8muO8MH/xdgAF+gE91daYKQAAAAAElFTkSuQmCC" style="height:41px;">\n- </a>\n- <strong>\n- <a href="http://multiqc.info" target="_blank">MultiQC v0.6</a>\n- </strong>\n- - Written by <a href="http://phil.ewels.co.uk" target="_blank">Phil Ewels</a>,\n- available on <a href="https://github.com/ewels/MultiQC" target="_blank">GitHub</a>.\n-</p>\n-<p>\n- This report uses <a href="http://www.highcharts.com/" target="_blank">HighCharts</a>,\n- <a href="https://jquery.com/" target="_blank">jQuery</a>,\n- <a href="http://getbootstrap.com/" target="_blank">Bootstrap</a>,\n- <a href="https://github.com/gka/chroma.js" target="_blank">chroma.js</a>\n- and <a href="http://bootstraptour.com/" target="_blank">Bootstrap Tour</a>.\n-</p>\n- </div>\n-</div>\n-\n-\n-\n-\n-<!-- Regex Help Modal -->\n-<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n- <div class="modal-dialog" role="document">\n- <div class="modal-content">\n- <div class="modal-header">\n- <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n- <h3 class="modal-title">Regex Help</h3>\n- </div>\n- <div class="modal-body">\n- <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n- <div class="row">\n- <div class="col-sm-6 regex_example_buttons">\n- <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n- <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n- <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n- <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n- <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n- <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n- <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n- <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n- <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n- <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n- <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n- <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n- <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n- </div>\n- <div class="col-sm-6 regex_example_demo">\n- <input type="text" class="form-control" />\n-<pre>\n-<span>samp_1</span>\n-<span>samp_1_edited</span>\n-<span>samp_2</span>\n-<span>samp_2_edited</span>\n-<span>samp_3</span>\n-<span>samp_3_edited</span>\n-<span>prepended_samp_1</span>\n-<span>tmp_samp_1_edited</span>\n-<span>tmpp_samp_1_edited</span>\n-<span>tmppp_samp_1_edited</span>\n-<span>#samp_1_edited.tmp</span>\n-<span>samp_11</span>\n-<span>samp_11111</span>\n-</pre>\n- <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n- </div>\n- </div>\n- </div>\n- <div class="modal-footer">\n- <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n- </div>\n- </div>\n- </div>\n-</div>\n-\n-</body>\n-</html>\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/report_samtools.html --- a/test-data/report_samtools.html Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,3468 +0,0 @@\n-<!DOCTYPE html>\n-<html lang="en">\n-<head>\n- \n- \n-\n-<meta charset="utf-8">\n-<meta http-equiv="X-UA-Compatible" content="IE=edge">\n-<meta name="viewport" content="width=device-width, initial-scale=1">\n-\n-<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n-<meta name="author" content="MultiQC">\n-<title>MultiQC Report</title>\n-\n-<!-- early variable initialisation -->\n-<script type="text/javascript">mqc_plots = {}; num_datasets_plot_limit = 50;</script>\n- \n- \n-\n-<!-- Favicon includes -->\n-<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,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">\n-<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,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'..b'HZC5D95fQRlgqDCd9PssvDD8aS7JwmmqHimkXQCSKTlZ6DzG+OrlIOg5An9rwc8YVDIBkMjuE7RPY0Kj9DTgcdXzRny85gC99vstOxRymPxjOY8N0kexZpR0NZQPnlc15Uw2DCdxtbuOdx9OPgTnl4hDz2a8muO8MH/xdgAF+gE91daYKQAAAAAElFTkSuQmCC" style="height:41px;">\n- </a>\n- <strong>\n- <a href="http://multiqc.info" target="_blank">MultiQC v0.6</a>\n- </strong>\n- - Written by <a href="http://phil.ewels.co.uk" target="_blank">Phil Ewels</a>,\n- available on <a href="https://github.com/ewels/MultiQC" target="_blank">GitHub</a>.\n-</p>\n-<p>\n- This report uses <a href="http://www.highcharts.com/" target="_blank">HighCharts</a>,\n- <a href="https://jquery.com/" target="_blank">jQuery</a>,\n- <a href="http://getbootstrap.com/" target="_blank">Bootstrap</a>,\n- <a href="https://github.com/gka/chroma.js" target="_blank">chroma.js</a>\n- and <a href="http://bootstraptour.com/" target="_blank">Bootstrap Tour</a>.\n-</p>\n- </div>\n-</div>\n-\n-\n-\n-\n-<!-- Regex Help Modal -->\n-<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n- <div class="modal-dialog" role="document">\n- <div class="modal-content">\n- <div class="modal-header">\n- <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n- <h3 class="modal-title">Regex Help</h3>\n- </div>\n- <div class="modal-body">\n- <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n- <div class="row">\n- <div class="col-sm-6 regex_example_buttons">\n- <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n- <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n- <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n- <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n- <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n- <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n- <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n- <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n- <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n- <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n- <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n- <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n- <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n- </div>\n- <div class="col-sm-6 regex_example_demo">\n- <input type="text" class="form-control" />\n-<pre>\n-<span>samp_1</span>\n-<span>samp_1_edited</span>\n-<span>samp_2</span>\n-<span>samp_2_edited</span>\n-<span>samp_3</span>\n-<span>samp_3_edited</span>\n-<span>prepended_samp_1</span>\n-<span>tmp_samp_1_edited</span>\n-<span>tmpp_samp_1_edited</span>\n-<span>tmppp_samp_1_edited</span>\n-<span>#samp_1_edited.tmp</span>\n-<span>samp_11</span>\n-<span>samp_11111</span>\n-</pre>\n- <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n- </div>\n- </div>\n- </div>\n- <div class="modal-footer">\n- <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n- </div>\n- </div>\n- </div>\n-</div>\n-\n-</body>\n-</html>\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/report_tophat.html --- a/test-data/report_tophat.html Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,3409 +0,0 @@\n-<!DOCTYPE html>\n-<html lang="en">\n-<head>\n- \n- \n-\n-<meta charset="utf-8">\n-<meta http-equiv="X-UA-Compatible" content="IE=edge">\n-<meta name="viewport" content="width=device-width, initial-scale=1">\n-\n-<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n-<meta name="author" content="MultiQC">\n-<title>MultiQC Report</title>\n-\n-<!-- early variable initialisation -->\n-<script type="text/javascript">mqc_plots = {}; num_datasets_plot_limit = 50;</script>\n- \n- \n-\n-<!-- Favicon includes -->\n-<link rel="icon" type="image/png" sizes="32x32" href="data:image/png;base64,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">\n-<link rel="icon" type="image/png" sizes="96x96" href="data:image/png;base64,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'..b'HZC5D95fQRlgqDCd9PssvDD8aS7JwmmqHimkXQCSKTlZ6DzG+OrlIOg5An9rwc8YVDIBkMjuE7RPY0Kj9DTgcdXzRny85gC99vstOxRymPxjOY8N0kexZpR0NZQPnlc15Uw2DCdxtbuOdx9OPgTnl4hDz2a8muO8MH/xdgAF+gE91daYKQAAAAAElFTkSuQmCC" style="height:41px;">\n- </a>\n- <strong>\n- <a href="http://multiqc.info" target="_blank">MultiQC v0.6</a>\n- </strong>\n- - Written by <a href="http://phil.ewels.co.uk" target="_blank">Phil Ewels</a>,\n- available on <a href="https://github.com/ewels/MultiQC" target="_blank">GitHub</a>.\n-</p>\n-<p>\n- This report uses <a href="http://www.highcharts.com/" target="_blank">HighCharts</a>,\n- <a href="https://jquery.com/" target="_blank">jQuery</a>,\n- <a href="http://getbootstrap.com/" target="_blank">Bootstrap</a>,\n- <a href="https://github.com/gka/chroma.js" target="_blank">chroma.js</a>\n- and <a href="http://bootstraptour.com/" target="_blank">Bootstrap Tour</a>.\n-</p>\n- </div>\n-</div>\n-\n-\n-\n-\n-<!-- Regex Help Modal -->\n-<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n- <div class="modal-dialog" role="document">\n- <div class="modal-content">\n- <div class="modal-header">\n- <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n- <h3 class="modal-title">Regex Help</h3>\n- </div>\n- <div class="modal-body">\n- <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n- <div class="row">\n- <div class="col-sm-6 regex_example_buttons">\n- <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n- <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n- <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n- <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n- <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n- <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n- <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n- <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n- <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n- <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n- <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n- <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n- <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n- </div>\n- <div class="col-sm-6 regex_example_demo">\n- <input type="text" class="form-control" />\n-<pre>\n-<span>samp_1</span>\n-<span>samp_1_edited</span>\n-<span>samp_2</span>\n-<span>samp_2_edited</span>\n-<span>samp_3</span>\n-<span>samp_3_edited</span>\n-<span>prepended_samp_1</span>\n-<span>tmp_samp_1_edited</span>\n-<span>tmpp_samp_1_edited</span>\n-<span>tmppp_samp_1_edited</span>\n-<span>#samp_1_edited.tmp</span>\n-<span>samp_11</span>\n-<span>samp_11111</span>\n-</pre>\n- <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n- </div>\n- </div>\n- </div>\n- <div class="modal-footer">\n- <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n- </div>\n- </div>\n- </div>\n-</div>\n-\n-</body>\n-</html>\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/samtools_data.txt --- a/test-data/samtools_data.txt Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,9736 +0,0 @@\n-# This file was produced by samtools stats (1.2+htslib-1.2.1) and can be plotted using plot-bamstats\n-# The command line was: stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /omaha-beach/cloud_26/files/000/dataset_20.dat /omaha-beach/cloud_26/files/000/dataset_114.dat\n-# CHK, Checksum\t[2]Read Names\t[3]Sequences\t[4]Qualities\n-# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)\n-CHK\t7742088d\t2cf80e59\t99341a6a\n-# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.\n-SN\traw total sequences:\t641821\n-SN\tfiltered sequences:\t0\n-SN\tsequences:\t641821\n-SN\tis sorted:\t1\n-SN\t1st fragments:\t320981\n-SN\tlast fragments:\t320840\n-SN\treads mapped:\t641821\n-SN\treads mapped and paired:\t638746\t# paired-end technology bit set + both mates mapped\n-SN\treads unmapped:\t0\n-SN\treads properly paired:\t635626\t# proper-pair bit set\n-SN\treads paired:\t641821\t# paired-end technology bit set\n-SN\treads duplicated:\t0\t# PCR or optical duplicate bit set\n-SN\treads MQ0:\t70\t# mapped and MQ=0\n-SN\treads QC failed:\t0\n-SN\tnon-primary alignments:\t12111\n-SN\ttotal length:\t64823921\t# ignores clipping\n-SN\tbases mapped:\t64823921\t# ignores clipping\n-SN\tbases mapped (cigar):\t64823921\t# more accurate\n-SN\tbases trimmed:\t0\n-SN\tbases duplicated:\t0\n-SN\tmismatches:\t275405\t# from NM fields\n-SN\terror rate:\t4.248509e-03\t# mismatches / bases mapped (cigar)\n-SN\taverage length:\t101\n-SN\tmaximum length:\t101\n-SN\taverage quality:\t26.0\n-SN\tinsert size average:\t719.7\n-SN\tinsert size standard deviation:\t1223.0\n-SN\tinward oriented pairs:\t317512\n-SN\toutward oriented pairs:\t1294\n-SN\tpairs with other orientation:\t30\n-SN\tpairs on different chromosomes:\t0\n-# First Fragment Qualitites. Use `grep ^FFQ | cut -f 2-` to extract this part.\n-# Columns correspond to qualities and rows to cycles. First column is the cycle number.\n-FFQ\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t113\t0\t0\t0\t0\t320725\t143\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-FFQ\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t4\t320810\t71\t91\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-FFQ\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t3\t320877\t25\t75\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-FFQ\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t5\t320905\t26\t44\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-FFQ\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t8\t320816\t67\t86\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-FFQ\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t0\t0\t0\t8\t320839\t42\t84\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-FFQ\t7\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t0\t0\t0\t6\t320867\t57\t47\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-FFQ\t8\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t8\t320845\t59\t64\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-FFQ\t9\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t2\t320851\t46\t78\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-FFQ\t10\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t4\t320836\t57\t77\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-FFQ\t11\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t7\t0\t0\t0\t0\t7\t320849\t46\t67\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-FFQ\t12\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t8\t320812\t80\t78\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-FFQ\t13\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t9\t320826\t56\t82\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-FFQ\t14\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t1\t0\t0\t0\t10\t320774\t77\t107\t7\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-FFQ\t15\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t8\t0\t0\t0\t0\t7\t320808\t60\t95\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-FFQ\t16\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t7\t1\t0\t0\t0\t12\t320786\t68\t101\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-FFQ\t17\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t8\t320758\t89\t116\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-FFQ\t18\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t6\t0\t0\t0\t0\t9\t320768\t86\t106\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-FFQ\t19\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t12\t320795\t77\t91\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-FFQ\t20\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t8\t0\t0\t0\t0\t11\t320739\t99\t110\t14\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-FFQ\t21\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t16\t320681\t115\t143\t21\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n-FFQ\t22\t0\t0\t0\t0\t'..b'92-892]\t892\t9\n-COV\t[893-893]\t893\t9\n-COV\t[894-894]\t894\t12\n-COV\t[895-895]\t895\t16\n-COV\t[896-896]\t896\t10\n-COV\t[897-897]\t897\t8\n-COV\t[898-898]\t898\t8\n-COV\t[899-899]\t899\t11\n-COV\t[900-900]\t900\t7\n-COV\t[901-901]\t901\t15\n-COV\t[902-902]\t902\t13\n-COV\t[903-903]\t903\t17\n-COV\t[904-904]\t904\t9\n-COV\t[905-905]\t905\t8\n-COV\t[906-906]\t906\t13\n-COV\t[907-907]\t907\t10\n-COV\t[908-908]\t908\t8\n-COV\t[909-909]\t909\t13\n-COV\t[910-910]\t910\t7\n-COV\t[911-911]\t911\t9\n-COV\t[912-912]\t912\t8\n-COV\t[913-913]\t913\t9\n-COV\t[914-914]\t914\t8\n-COV\t[915-915]\t915\t9\n-COV\t[916-916]\t916\t6\n-COV\t[917-917]\t917\t9\n-COV\t[918-918]\t918\t7\n-COV\t[919-919]\t919\t9\n-COV\t[920-920]\t920\t8\n-COV\t[921-921]\t921\t13\n-COV\t[922-922]\t922\t5\n-COV\t[923-923]\t923\t5\n-COV\t[924-924]\t924\t5\n-COV\t[925-925]\t925\t7\n-COV\t[926-926]\t926\t10\n-COV\t[927-927]\t927\t6\n-COV\t[928-928]\t928\t21\n-COV\t[929-929]\t929\t10\n-COV\t[930-930]\t930\t10\n-COV\t[931-931]\t931\t7\n-COV\t[932-932]\t932\t12\n-COV\t[933-933]\t933\t14\n-COV\t[934-934]\t934\t14\n-COV\t[935-935]\t935\t7\n-COV\t[936-936]\t936\t12\n-COV\t[937-937]\t937\t13\n-COV\t[938-938]\t938\t10\n-COV\t[939-939]\t939\t12\n-COV\t[940-940]\t940\t18\n-COV\t[941-941]\t941\t11\n-COV\t[942-942]\t942\t10\n-COV\t[943-943]\t943\t6\n-COV\t[944-944]\t944\t12\n-COV\t[945-945]\t945\t12\n-COV\t[946-946]\t946\t8\n-COV\t[947-947]\t947\t12\n-COV\t[948-948]\t948\t10\n-COV\t[949-949]\t949\t5\n-COV\t[950-950]\t950\t9\n-COV\t[951-951]\t951\t16\n-COV\t[952-952]\t952\t13\n-COV\t[953-953]\t953\t15\n-COV\t[954-954]\t954\t15\n-COV\t[955-955]\t955\t8\n-COV\t[956-956]\t956\t15\n-COV\t[957-957]\t957\t18\n-COV\t[958-958]\t958\t9\n-COV\t[959-959]\t959\t21\n-COV\t[960-960]\t960\t14\n-COV\t[961-961]\t961\t17\n-COV\t[962-962]\t962\t9\n-COV\t[963-963]\t963\t14\n-COV\t[964-964]\t964\t6\n-COV\t[965-965]\t965\t5\n-COV\t[966-966]\t966\t13\n-COV\t[967-967]\t967\t12\n-COV\t[968-968]\t968\t13\n-COV\t[969-969]\t969\t10\n-COV\t[970-970]\t970\t13\n-COV\t[971-971]\t971\t8\n-COV\t[972-972]\t972\t13\n-COV\t[973-973]\t973\t12\n-COV\t[974-974]\t974\t14\n-COV\t[975-975]\t975\t9\n-COV\t[976-976]\t976\t12\n-COV\t[977-977]\t977\t4\n-COV\t[978-978]\t978\t14\n-COV\t[979-979]\t979\t6\n-COV\t[980-980]\t980\t12\n-COV\t[981-981]\t981\t5\n-COV\t[982-982]\t982\t8\n-COV\t[983-983]\t983\t4\n-COV\t[984-984]\t984\t9\n-COV\t[985-985]\t985\t9\n-COV\t[986-986]\t986\t10\n-COV\t[987-987]\t987\t8\n-COV\t[988-988]\t988\t4\n-COV\t[989-989]\t989\t6\n-COV\t[990-990]\t990\t3\n-COV\t[991-991]\t991\t5\n-COV\t[992-992]\t992\t2\n-COV\t[993-993]\t993\t6\n-COV\t[994-994]\t994\t6\n-COV\t[995-995]\t995\t7\n-COV\t[996-996]\t996\t14\n-COV\t[997-997]\t997\t12\n-COV\t[998-998]\t998\t7\n-COV\t[999-999]\t999\t8\n-COV\t[1000-1000]\t1000\t8\n-COV\t[1000<]\t1000\t5025\n-# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile\n-GCD\t0.0\t0.554\t0.000\t0.000\t0.000\t0.000\t0.000\n-GCD\t0.5\t0.831\t0.525\t0.525\t0.525\t0.525\t0.525\n-GCD\t36.0\t1.385\t0.954\t0.954\t0.954\t1.490\t1.490\n-GCD\t37.0\t2.216\t2.495\t2.495\t4.146\t6.560\t6.560\n-GCD\t38.0\t5.263\t0.247\t0.454\t3.520\t5.868\t9.883\n-GCD\t39.0\t9.141\t0.177\t0.303\t2.161\t8.777\t12.812\n-GCD\t40.0\t12.188\t0.020\t1.192\t9.060\t22.018\t27.371\n-GCD\t41.0\t16.343\t0.035\t0.550\t2.702\t11.469\t12.908\n-GCD\t42.0\t21.884\t0.010\t0.172\t2.121\t5.621\t17.094\n-GCD\t43.0\t28.255\t0.010\t0.328\t1.449\t4.277\t10.166\n-GCD\t44.0\t36.288\t0.162\t0.394\t5.484\t15.145\t50.490\n-GCD\t45.0\t42.105\t0.020\t0.131\t1.252\t7.009\t17.811\n-GCD\t46.0\t49.861\t0.015\t0.121\t0.636\t1.939\t37.506\n-GCD\t47.0\t56.510\t0.030\t0.141\t1.015\t4.500\t6.338\n-GCD\t48.0\t64.543\t0.010\t0.091\t2.565\t7.287\t21.872\n-GCD\t49.0\t68.975\t0.010\t0.333\t0.672\t10.751\t27.129\n-GCD\t50.0\t73.407\t0.010\t0.121\t1.358\t3.883\t6.615\n-GCD\t51.0\t77.008\t0.121\t0.576\t1.576\t4.363\t13.923\n-GCD\t52.0\t81.994\t0.010\t0.086\t1.560\t4.414\t109.383\n-GCD\t53.0\t84.488\t0.040\t0.071\t0.500\t3.025\t31.234\n-GCD\t54.0\t86.704\t0.020\t0.313\t9.332\t39.683\t203.959\n-GCD\t55.0\t89.197\t0.005\t0.051\t1.268\t5.045\t23.578\n-GCD\t56.0\t91.136\t0.071\t0.192\t1.566\t9.994\t33.315\n-GCD\t57.0\t94.460\t0.040\t0.348\t1.167\t5.050\t11.660\n-GCD\t58.0\t95.845\t0.131\t0.131\t1.899\t2.742\t4.929\n-GCD\t59.0\t96.399\t3.313\t3.313\t3.313\t3.666\t3.666\n-GCD\t60.0\t97.507\t0.995\t0.995\t5.176\t6.954\t33.234\n-GCD\t61.0\t98.338\t1.591\t1.591\t1.788\t4.848\t4.848\n-GCD\t62.0\t98.892\t3.171\t3.171\t3.171\t7.343\t7.343\n-GCD\t63.0\t99.446\t0.530\t0.530\t0.530\t6.403\t6.403\n-GCD\t64.0\t100.000\t1.025\t1.025\t1.025\t4.585\t4.585\n' |
| b |
| diff -r 66f1187ed363 -r 4612d775965f test-data/tophat_data.txt --- a/test-data/tophat_data.txt Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,14 +0,0 @@ -Left reads: - Input : 316390 - Mapped : 314921 (99.5% of input) - of these: 5715 ( 1.8%) have multiple alignments (0 have >20) -Right reads: - Input : 316390 - Mapped : 314789 (99.5% of input) - of these: 5707 ( 1.8%) have multiple alignments (0 have >20) -99.5% overall read mapping rate. - -Aligned pairs: 313405 - of these: 5638 ( 1.8%) have multiple alignments - 34 ( 0.0%) are discordant alignments -99.0% concordant pair alignment rate. |
| b |
| diff -r 66f1187ed363 -r 4612d775965f tool_dependencies.xml --- a/tool_dependencies.xml Tue Oct 04 04:02:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="multiqc" version="0.6"> - <repository changeset_revision="68eebe70b537" name="package_multiqc_0_6" owner="engineson" toolshed="http://toolshed.g2.bx.psu.edu" /> - </package> - <package name="libpng" version="1.6.7"> - <repository changeset_revision="588666932a32" name="package_libpng_1_6_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |