| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/3.1.1.0 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.1 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/2.18.2.0 |
| toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_CollectRnaSeqMetrics/1.126.0 |
| picard_CollectRnaSeqMetrics |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| picard | 2.18.2 | package |
| r-base | 3.4.1 | package |
| ucsc-gff3togenepred | 357 | package |
| ucsc-gtftogenepred | 357 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
inputFile: picard_CollectRnaSeqMetrics.bam reference_source|ref_file: picard_CollectRnaSeqMetrics_ref.fa reference_source|reference_source_selector: history gene_reference_source|refFlat: picard_CollectRnaSeqMetrics.refFlat gene_reference_source|gene_reference_source_selector: refflat strand_specificity: NONE minimum_length: 500 rrna_fragment_percentage: 0.8 metric_accumulation_level: ALL_READS assume_sorted: True |
name: value |
picard_CollectRnaSeqMetrics.bam picard_CollectRnaSeqMetrics_ref.fa picard_CollectRnaSeqMetrics.refFlat value |
| Test-2 |
inputFile: picard_CollectRnaSeqMetrics.bam reference_source|ref_file: picard_CollectRnaSeqMetrics_ref.fa reference_source|reference_source_selector: history gene_reference_source|refFlat: picard_CollectRnaSeqMetrics.ucsc_output gene_reference_source|gene_reference_source_selector: refflat strand_specificity: NONE minimum_length: 500 rrna_fragment_percentage: 0.8 metric_accumulation_level: ALL_READS assume_sorted: True |
name: value |
picard_CollectRnaSeqMetrics.bam picard_CollectRnaSeqMetrics_ref.fa picard_CollectRnaSeqMetrics.ucsc_output value |
| Test-3 |
inputFile: picard_CollectRnaSeqMetrics.bam reference_source|ref_file: picard_CollectRnaSeqMetrics_ref.fa reference_source|reference_source_selector: history gene_reference_source|refFlat: picard_CollectRnaSeqMetrics.gtf gene_reference_source|gene_reference_source_selector: gtf strand_specificity: NONE minimum_length: 500 rrna_fragment_percentage: 0.8 metric_accumulation_level: ALL_READS assume_sorted: True |
name: value |
picard_CollectRnaSeqMetrics.bam picard_CollectRnaSeqMetrics_ref.fa picard_CollectRnaSeqMetrics.gtf value |
| Test-4 |
inputFile: picard_CollectRnaSeqMetrics.bam reference_source|ref_file: picard_CollectRnaSeqMetrics_ref.fa reference_source|reference_source_selector: history gene_reference_source|refFlat: picard_CollectRnaSeqMetrics.gff3 gene_reference_source|gene_reference_source_selector: gtf strand_specificity: NONE minimum_length: 500 rrna_fragment_percentage: 0.8 metric_accumulation_level: ALL_READS assume_sorted: True |
name: value |
picard_CollectRnaSeqMetrics.bam picard_CollectRnaSeqMetrics_ref.fa picard_CollectRnaSeqMetrics.gff3 value |