Repository revision
23:abfd8a6544d7

Repository 'multiqc'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/multiqc

MultiQC tool metadata
Miscellaneous
MultiQC
aggregate results from bioinformatics analyses into a single report
multiqc
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
1.11+galaxy1
multiqc --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7.1
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.5.2
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.5.1
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.5.0
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.3.1
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.2.1
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.2.0
multiqc
Requirements (dependencies defined in the <requirements> tag set)
name version type
multiqc 1.11 package
Functional tests
name inputs outputs required files
Test-1 results_0|software_cond|input: cutadapt.txt
results_0|software_cond|software: cutadapt
results_1|software_cond|input: ['fastp1.json.txt', 'fastp2.json.txt']
results_1|software_cond|software: fastp
results_2|software_cond|output_0|type: data
results_2|software_cond|output_0|input: ['fastqc_1.txt', 'fastqc_2.txt']
results_2|software_cond|software: fastqc
results_3|software_cond|input: flexbar.txt
results_3|software_cond|software: flexbar
results_4|software_cond|input: ['slamdunk_summary.txt', 'slamdunk_reads1_overallrates.csv', 'slamdunk_reads2_overallrates.csv']
results_4|software_cond|software: slamdunk
results_5|software_cond|input: sortmerna.txt
results_5|software_cond|software: sortmerna
results_6|software_cond|input: trimmomatic.txt
results_6|software_cond|software: trimmomatic
title: Title of the report
comment: Commment for the report
flat: True
export: True
saveLog: True
name: value
name: value
cutadapt.txt
fastp1.json.txt
fastp2.json.txt
fastqc_1.txt
fastqc_2.txt
flexbar.txt
slamdunk_summary.txt
slamdunk_reads1_overallrates.csv
slamdunk_reads2_overallrates.csv
sortmerna.txt
trimmomatic.txt
value
Test-2 results_0|software_cond|output_0|type: align
results_0|software_cond|output_0|input: bismark.txt
results_0|software_cond|software: bismark
results_1|software_cond|input: ['bowtie2_1.txt', 'bowtie2_2.txt']
results_1|software_cond|software: bowtie2
results_2|software_cond|input: ['hisat2_1.txt', 'hisat2_2.txt']
results_2|software_cond|software: hisat2
results_3|software_cond|input: ['hicexplorer1.log', 'hicexplorer1.log', 'hicexplorer2.log']
results_3|software_cond|software: hicexplorer
results_4|software_cond|input: ['kallisto_1.txt', 'kallisto_2.txt']
results_4|software_cond|software: kallisto
results_5|software_cond|input: ['macs_1.txt', 'macs_2.txt']
results_5|software_cond|software: macs2
results_6|software_cond|output_0|type|input: star_log.txt
results_6|software_cond|output_0|type|type: log
results_6|software_cond|output_1|type|input: star_counts.txt
results_6|software_cond|output_1|type|type: genecounts
results_6|software_cond|software: star
results_7|software_cond|input: tophat.txt
results_7|software_cond|software: tophat
saveLog: False
name: value
bismark.txt
bowtie2_1.txt
bowtie2_2.txt
hisat2_1.txt
hisat2_2.txt
hicexplorer1.log
hicexplorer2.log
kallisto_1.txt
kallisto_2.txt
macs_1.txt
macs_2.txt
star_log.txt
star_counts.txt
tophat.txt
value
Test-3 results_0|software_cond|input: bamtools.txt
results_0|software_cond|software: bamtools
results_1|software_cond|input: bcftools.txt
results_1|software_cond|software: bcftools
results_2|software_cond|input: busco.txt
results_2|software_cond|software: busco
results_3|software_cond|output_0|type: bamPEFragmentSize
results_3|software_cond|output_0|input: deeptools_bamPEFragmentSize.txt
results_3|software_cond|output_1|type: estimateReadFiltering
results_3|software_cond|output_1|input: deeptools_estimateReadFiltering.txt
results_3|software_cond|output_2|type: plotCoverageStdout
results_3|software_cond|output_2|input: deeptools_plotCoverageStdout.txt
results_3|software_cond|output_3|type: plotCoverageOutRawCounts
results_3|software_cond|output_3|input: deeptools_plotCoverageOutRawCounts.txt
results_3|software_cond|output_4|type: plotEnrichment
results_3|software_cond|output_4|input: deeptools_plotEnrichment.txt
results_3|software_cond|output_5|type: plotFingerprintOutRawCounts
results_3|software_cond|output_5|input: deeptools_plotFingerprintOutRawCounts.txt
results_3|software_cond|software: deeptools
results_4|software_cond|input: featureCounts.txt
results_4|software_cond|software: featureCounts
results_5|software_cond|output_0|type: base_recalibrator
results_5|software_cond|output_0|input: gatk_BaseRecalibrator.txt
results_5|software_cond|output_1|type: varianteval
results_5|software_cond|output_1|input: gatk_varianteval.txt
results_5|software_cond|software: gatk
results_6|software_cond|input: htseq.txt
results_6|software_cond|software: htseq
results_7|software_cond|output_0|type: gcbias
results_7|software_cond|output_0|input: picard_collectGcBias.txt
results_7|software_cond|output_1|type: insertsize
results_7|software_cond|output_1|input: picard_CollectInsertSizeMetrics.txt
results_7|software_cond|output_2|type: markdups
results_7|software_cond|output_2|input: picard_MarkDuplicates.txt
results_7|software_cond|output_3|type: basedistributionbycycle
results_7|software_cond|output_3|input: picard_CollectBaseDistributionByCycle.txt
results_7|software_cond|output_4|type: rnaseqmetrics
results_7|software_cond|output_4|input: picard_CollectRnaSeqMetrics.txt
results_7|software_cond|output_5|type: alignment_metrics
results_7|software_cond|output_5|input: picard_CollectAlignmentSummaryMetrics.txt
results_7|software_cond|software: picard
results_8|software_cond|input: ['prokka_1.txt', 'prokka_2.txt']
results_8|software_cond|software: prokka
results_9|software_cond|input: genome_results.txt
results_9|software_cond|software: qualimap
results_10|software_cond|input: quast.tsv
results_10|software_cond|software: quast
results_11|software_cond|output_0|type|input: rseqc.txt
results_11|software_cond|output_0|type|type: read_gc
results_11|software_cond|software: rseqc
results_12|software_cond|input: samblaster.txt
results_12|software_cond|software: samblaster
results_13|software_cond|output_0|type|input: samtools_stats.txt
results_13|software_cond|output_0|type|type: stats
results_13|software_cond|output_1|type|input: samtools_flagstat.txt
results_13|software_cond|output_1|type|type: flagstat
results_13|software_cond|output_2|type|input: samtools_idxstats.txt
results_13|software_cond|output_2|type|type: idxstats
results_13|software_cond|software: samtools
results_14|software_cond|input: snpeff.csv
results_14|software_cond|software: snpeff
results_15|software_cond|output_0|type|input: vcftools.txt
results_15|software_cond|output_0|type|type: tstv_by_qual
results_15|software_cond|software: vcftools
name: value
bamtools.txt
bcftools.txt
busco.txt
deeptools_bamPEFragmentSize.txt
deeptools_estimateReadFiltering.txt
deeptools_plotCoverageStdout.txt
deeptools_plotCoverageOutRawCounts.txt
deeptools_plotEnrichment.txt
deeptools_plotFingerprintOutRawCounts.txt
featureCounts.txt
gatk_BaseRecalibrator.txt
gatk_varianteval.txt
htseq.txt
picard_collectGcBias.txt
picard_CollectInsertSizeMetrics.txt
picard_MarkDuplicates.txt
picard_CollectBaseDistributionByCycle.txt
picard_CollectRnaSeqMetrics.txt
picard_CollectAlignmentSummaryMetrics.txt
prokka_1.txt
prokka_2.txt
genome_results.txt
quast.tsv
rseqc.txt
samblaster.txt
samtools_stats.txt
samtools_flagstat.txt
samtools_idxstats.txt
snpeff.csv
vcftools.txt
value
Test-4 results_0|software_cond|plot_type: linegraph
results_0|software_cond|section_name: BPC
results_0|software_cond|description: Sum of intensity (Y) of the most intense peaks at each retention time(X)
results_0|software_cond|xlab: Retention Time
results_0|software_cond|ylab: Base Peak Intensity
results_0|software_cond|input: ['cc_ko15.bpc.tab', 'cc_wt15.bpc.tab']
results_0|software_cond|software: custom_content
name: value
cc_ko15.bpc.tab
cc_wt15.bpc.tab
value
Test-5 results_0|software_cond|output_0|type: data
results_0|software_cond|output_0|input: ['fastqc_1.txt', 'fastqc_2.txt']
results_0|software_cond|software: fastqc
title: Title of the report
comment: Commment for the report
flat: True
export: True
name: value
fastqc_1.txt
fastqc_2.txt
value
Test-6 results_0|software_cond|input: pycoqc.json
results_0|software_cond|software: pycoqc
title: Title of the report
comment: Commment for the report
name: value
pycoqc.json
value
Test-7 results_0|software_cond|output_0|type|input: junction_annotation.txt
results_0|software_cond|output_0|type|type: junction_annotation
results_0|software_cond|output_1|type|input: junction_saturation.txt
results_0|software_cond|output_1|type|type: junction_saturation
results_0|software_cond|software: rseqc
title: RSEQC report
name: value
junction_annotation.txt
junction_saturation.txt
value