| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy4 |
| toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy3 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 |
| 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 | 1.27 | 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 |
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 |
name: value 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 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 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 name: value |
pycoqc.json value |
| Test-7 |
results_0|software_cond|input: bcftools.txt results_0|software_cond|software: bcftools title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
bcftools.txt value |
| Test-8 |
results_0|software_cond|input: ['bowtie2_1.txt', 'bowtie2_2.txt'] results_0|software_cond|software: bowtie2 title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
bowtie2_1.txt bowtie2_2.txt value |
| Test-9 |
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 name: value |
fastqc_1.txt fastqc_2.txt value |
| Test-10 |
results_0|software_cond|input: trimmomatic.txt results_0|software_cond|software: trimmomatic title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
trimmomatic.txt value |
| Test-11 |
results_0|software_cond|input: flexbar.txt results_0|software_cond|software: flexbar title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
flexbar.txt value |
| Test-12 |
results_0|software_cond|input: ['fastp1.json.txt', 'fastp2.json.txt'] results_0|software_cond|software: fastp title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
fastp1.json.txt fastp2.json.txt value |
| Test-13 |
results_0|software_cond|output_0|type: align results_0|software_cond|output_0|input: bismark.txt results_0|software_cond|software: bismark title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
bismark.txt value |
| Test-14 |
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: Title of the report comment: Commment for the report flat: True export: True |
name: value |
junction_annotation.txt junction_saturation.txt value |
| Test-15 |
results_0|software_cond|output_0|type|input: star_log.txt results_0|software_cond|output_0|type|type: log results_0|software_cond|output_1|type|input: star_counts.txt results_0|software_cond|output_1|type|type: genecounts results_0|software_cond|software: star title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
star_log.txt star_counts.txt value |
| Test-16 |
results_0|software_cond|input: cutadapt.txt results_0|software_cond|software: cutadapt title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
cutadapt.txt value |
| Test-17 |
results_0|software_cond|output_0|type|input: samtools_stats.txt results_0|software_cond|output_0|type|type: stats results_0|software_cond|output_1|type|input: samtools_flagstat.txt results_0|software_cond|output_1|type|type: flagstat results_0|software_cond|output_2|type|input: samtools_idxstats.txt results_0|software_cond|output_2|type|type: idxstats results_0|software_cond|software: samtools title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
samtools_stats.txt samtools_flagstat.txt samtools_idxstats.txt value |
| Test-18 |
results_0|software_cond|input: busco.txt results_0|software_cond|software: busco title: Title of the report comment: Commment for the report flat: True export: True |
name: value |
busco.txt value |
| Test-19 |
results_0|software_cond|input: featureCounts.txt results_0|software_cond|software: featureCounts title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
featureCounts.txt value |
| Test-20 |
results_0|software_cond|output_0|type: gcbias results_0|software_cond|output_0|input: picard_collectGcBias.txt results_0|software_cond|output_1|type: insertsize results_0|software_cond|output_1|input: picard_CollectInsertSizeMetrics.txt results_0|software_cond|output_2|type: markdups results_0|software_cond|output_2|input: picard_MarkDuplicates.txt results_0|software_cond|output_3|type: basedistributionbycycle results_0|software_cond|output_3|input: picard_CollectBaseDistributionByCycle.txt results_0|software_cond|output_4|type: rnaseqmetrics results_0|software_cond|output_4|input: picard_CollectRnaSeqMetrics.txt results_0|software_cond|output_5|type: alignment_metrics results_0|software_cond|output_5|input: picard_CollectAlignmentSummaryMetrics.txt results_0|software_cond|software: picard title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
picard_collectGcBias.txt picard_CollectInsertSizeMetrics.txt picard_MarkDuplicates.txt picard_CollectBaseDistributionByCycle.txt picard_CollectRnaSeqMetrics.txt picard_CollectAlignmentSummaryMetrics.txt value |
| Test-21 |
results_0|software_cond|input: genome_results.txt results_0|software_cond|software: qualimap title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
genome_results.txt value |
| Test-22 |
results_0|software_cond|output_0|type: base_recalibrator results_0|software_cond|output_0|input: gatk_BaseRecalibrator.txt results_0|software_cond|output_1|type: varianteval results_0|software_cond|output_1|input: gatk_varianteval.txt results_0|software_cond|software: gatk title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
gatk_BaseRecalibrator.txt gatk_varianteval.txt value |
| Test-23 |
results_0|software_cond|input: bamtools.txt results_0|software_cond|software: bamtools title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
bamtools.txt value |
| Test-24 |
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 name: value |
pycoqc.json value |
| Test-25 |
results_0|software_cond|input: kraken_test0_report.tab results_0|software_cond|software: kraken title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
kraken_test0_report.tab value |
| Test-26 |
results_0|software_cond|input: diamond.log results_0|software_cond|software: diamond title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
diamond.log value |
| Test-27 |
results_0|software_cond|input: bakta.txt results_0|software_cond|software: bakta title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
bakta.txt value |
| Test-28 |
results_0|software_cond|input: freyja.tsv results_0|software_cond|software: freyja title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
freyja.tsv value |
| Test-29 |
results_0|software_cond|input: checkm.tabular results_0|software_cond|software: checkm title: Title of the report comment: Commment for the report flat: True export: True |
name: value |
checkm.tabular value |
| Test-30 |
results_0|software_cond|input: output_dedup_pairs.stats results_0|software_cond|software: pairtools title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
output_dedup_pairs.stats value |
| Test-31 |
results_0|software_cond|input: porechop.log results_0|software_cond|software: porechop image_content_input: test_image.png title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
porechop.log test_image.png value |
| Test-32 |
results_0|software_cond|input: snippy.txt results_0|software_cond|software: snippy title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
snippy.txt value |
| Test-33 |
results_0|software_cond|input: metaphlan.txt results_0|software_cond|software: metaphlan title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
metaphlan.txt value |
| Test-34 |
results_0|software_cond|input: bbduk.txt results_0|software_cond|software: bbduk title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
bbduk.txt value |
| Test-35 |
results_0|software_cond|input: megahit.txt results_0|software_cond|software: megahit title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
megahit.txt value |
| Test-36 |
results_0|software_cond|input: nonpareil.json results_0|software_cond|software: nonpareil title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
nonpareil.json value |
| Test-37 |
results_0|software_cond|input: gtdbtk.tsv results_0|software_cond|software: gtdbtk title: Title of the report comment: Commment for the report flat: True export: True |
name: value |
gtdbtk.tsv value |
| Test-38 |
results_0|software_cond|input: sambamba.txt results_0|software_cond|software: sambamba title: Title of the report comment: Commment for the report flat: True export: True |
name: value name: value |
sambamba.txt value |