| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy4 (this tool) |
| toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy3 |
| toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy1 |
| music_deconvolution |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| music-deconvolution | 0.1.1 | package |
| r-cowplot | 0.9.3 | package |
| r-reshape2 | 1.4.4 | package |
| r-ggdendro | 0.1_20 | package |
| Additional information about this tool |
cat '$conf' >> /dev/stderr &&
mkdir report_data &&
Rscript --vanilla '$__tool_directory__/scripts/${do.method}.R' '$conf'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
scrna_eset: Mousesubeset.degenesonly2.half.rds bulk_eset: Mousebulkeset.rds do|celltypes_label: cellType do|samples_label: sampleID do|celltypes: Endo,Podo,PT,LOH,DCT,CD-PC,CD-IC,Fib,Macro,Neutro,B lymph,T lymph,NK do|method: dendrogram |
name: value |
Mousesubeset.degenesonly2.half.rds Mousebulkeset.rds value |
| Test-2 |
scrna_eset: Mousesubeset.degenesonly2.half.rds bulk_eset: Mousebulkeset.rds do|celltypes_label: cellType do|samples_label: sampleID do|celltypes: Endo,Podo,PT,LOH,DCT,CD-PC,CD-IC,Fib,Macro,Neutro,B lymph,T lymph,NK do|cluster_groups_0|cluster_id: C1 do|cluster_groups_0|celltypes: Neutro do|cluster_groups_1|cluster_id: C2 do|cluster_groups_1|celltypes: Podo do|cluster_groups_2|cluster_id: C3 do|cluster_groups_2|celltypes: Endo,CD-PC,LOH,CD-IC,DCT,PT do|cluster_groups_2|marker_name: Epithelial do|cluster_groups_2|marker_list: epith.markers do|cluster_groups_3|cluster_id: C4 do|cluster_groups_3|celltypes: Macro,Fib,B lymph,NK,T lymph do|cluster_groups_3|marker_name: Immune do|cluster_groups_3|marker_list: immune.markers do|method: dendrogram |
name: value name: value |
Mousesubeset.degenesonly2.half.rds Mousebulkeset.rds epith.markers immune.markers value |
| Test-3 |
scrna_eset: EMTABesethealthy.subset.rds bulk_eset: GSE50244bulkeset.subset.rds do|est_methods: NNLS do|celltypes_label: cellType do|samples_label: sampleID do|method: estimateprops |
name: value |
EMTABesethealthy.subset.rds GSE50244bulkeset.subset.rds value |
| Test-4 |
scrna_eset: EMTABesethealthy.subset.rds bulk_eset: GSE50244bulkeset.subset.rds do|celltypes_label: cellType do|samples_label: sampleID do|method: estimateprops |
name: value |
EMTABesethealthy.subset.rds GSE50244bulkeset.subset.rds value |
| Test-5 |
scrna_eset: EMTABesethealthy.subset.rds bulk_eset: GSE50244bulkeset.subset.rds do|celltypes_label: cellType do|samples_label: sampleID do|celltypes: alpha,beta,delta,gamma,acinar,ductal do|disease_factor|phenotype_scrna_target: beta do|disease_factor|phenotype_target: hba1c do|disease_factor|phenotype_target_threshold: 6.5 do|disease_factor|sample_disease_group: T2D do|disease_factor|sample_disease_group_scale: 5 do|disease_factor|use: yes do|method: estimateprops |
name: value |
EMTABesethealthy.subset.rds GSE50244bulkeset.subset.rds value |