Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0 (this tool) |
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 |