| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.2.1 |
| toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.2.0 (this tool) |
| multiqc |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| multiqc | 1.2 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
results_0|software_cond|input: cutadapt.txt results_1|software_cond|software: fastqc results_4|software_cond|software: trimmomatic results_4|software_cond|input: trimmomatic.txt results_1|software_cond|output_0|input: ['fastqc_1.txt', 'fastqc_2.txt'] saveLog: True results_3|software_cond|software: sortmerna results_2|software_cond|input: flexbar.txt results_3|software_cond|input: sortmerna.txt results_0|software_cond|software: cutadapt results_2|software_cond|software: flexbar results_1|software_cond|output_0|type: data |
html_report: None log: pre_alignment_soft_log.txt |
cutadapt.txt fastqc_1.txt fastqc_2.txt flexbar.txt sortmerna.txt trimmomatic.txt pre_alignment_soft_log.txt |
| Test-2 |
results_4|software_cond|output_0|type|input: star_log.txt results_5|software_cond|input: tophat.txt results_1|software_cond|software: bowtie2 results_0|software_cond|output_0|type: align results_4|software_cond|software: star results_4|software_cond|output_1|type|type: genecounts results_4|software_cond|output_1|type|input: star_counts.txt results_4|software_cond|output_0|type|type: log results_0|software_cond|output_0|input: bismark.txt saveLog: False results_1|software_cond|input: ['bowtie2_1.txt', 'bowtie2_2.txt'] results_2|software_cond|input: ['hisat2_1.txt', 'hisat2_2.txt'] results_5|software_cond|software: tophat results_3|software_cond|input: ['kallisto_1.txt', 'kallisto_2.txt'] results_0|software_cond|software: bismark results_2|software_cond|software: hisat2 results_3|software_cond|software: kallisto |
html_report: None |
bismark.txt bowtie2_1.txt bowtie2_2.txt hisat2_1.txt hisat2_2.txt kallisto_1.txt kallisto_2.txt star_log.txt star_counts.txt tophat.txt |
| Test-3 |
results_5|software_cond|input: htseq.txt results_9|software_cond|software: rseqc results_6|software_cond|output_0|type: gcbias results_4|software_cond|output_1|type: varianteval results_6|software_cond|output_1|type: insertsize results_12|software_cond|output_0|type|type: tstv_by_qual results_6|software_cond|output_5|input: picard_CollectAlignmentSummaryMetrics.txt results_7|software_cond|software: prokka results_11|software_cond|output_0|type|type: stats results_12|software_cond|output_0|type|input: vcftools.txt results_3|software_cond|input: featureCounts.txt results_11|software_cond|output_2|type|type: idxstats results_6|software_cond|output_0|input: picard_collectGcBias.txt results_10|software_cond|software: samblaster results_4|software_cond|software: gatk results_6|software_cond|software: picard results_9|software_cond|output_0|type|type: read_gc results_6|software_cond|output_1|input: picard_CollectInsertSizeMetrics.txt results_6|software_cond|output_2|type: markdups results_12|software_cond|software: vcftools results_8|software_cond|software: quast results_7|software_cond|input: ['prokka_1.txt', 'prokka_2.txt'] results_11|software_cond|output_2|type|input: samtools_idxstats.txt results_6|software_cond|output_3|type: basedistributionbycycle results_10|software_cond|input: samblaster.txt results_1|software_cond|input: bcftools.txt results_4|software_cond|output_1|input: gatk_varianteval.txt results_11|software_cond|output_0|type|input: samtools_stats.txt results_11|software_cond|output_1|type|input: samtools_flagstat.txt results_11|software_cond|software: samtools results_0|software_cond|software: bamtools results_2|software_cond|software: busco results_6|software_cond|output_5|type: alignment_metrics results_0|software_cond|input: bamtools.txt results_11|software_cond|output_1|type|type: flagstat results_6|software_cond|output_4|type: rnaseqmetrics results_6|software_cond|output_4|input: picard_CollectRnaSeqMetrics.txt results_6|software_cond|output_3|input: picard_CollectBaseDistributionByCycle.txt results_6|software_cond|output_2|input: picard_MarkDuplicates.txt results_3|software_cond|software: featureCounts results_2|software_cond|input: busco.txt results_5|software_cond|software: htseq results_8|software_cond|input: quast.tsv results_4|software_cond|output_0|type: base_recalibrator results_1|software_cond|software: bcftools results_9|software_cond|output_0|type|input: rseqc.txt results_4|software_cond|output_0|input: gatk_BaseRecalibrator.txt |
html_report: None |
bamtools.txt bcftools.txt busco.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 quast.tsv rseqc.txt samblaster.txt samtools_stats.txt samtools_flagstat.txt samtools_idxstats.txt vcftools.txt |
| Test-4 |
results_0|software_cond|input: ['cc_ko15.bpc.tab', 'cc_wt15.bpc.tab'] results_0|software_cond|xlab: Retention Time results_0|software_cond|description: Sum of intensity (Y) of the most intense peaks at each retention time(X) results_0|software_cond|section_name: BPC results_0|software_cond|plot_type: linegraph results_0|software_cond|title: Base peak chromatogram results_0|software_cond|ylab: Base Peak Intensity results_0|software_cond|software: custom_content |
html_report: report_manual_custom_content.html |
cc_ko15.bpc.tab cc_wt15.bpc.tab report_manual_custom_content.html |