upload control methods

src/control_methods/negative/config.vsh.yaml

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+__merge__: ../../api/comp_control_method.yaml
+
+name: negative
+label: negative
+summary: A negative control method.
+description: |
+  A negative control method.
+# references:
+#   doi: 
+
+# info:
+#   documentation_url: https://xzhoulab.github.io/SRTsim
+#   repository_url: https://github.com/xzhoulab/srtsim
+
+resources:
+  - type: r_script
+    path: script.R
+
+engines:
+  - type: docker
+    image: openproblems/base_r:1.0.0
+    setup:
+      - type: r
+        cran: SRTsim
+
+runners:
+  - type: executable
+  - type: nextflow
+    directives:
+      label: [midtime, midmem, midcpu]

src/control_methods/negative/script.R

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+## VIASH START
+par <- list(
+  input = "resources_test/datasets/MOBNEW/dataset_sp.h5ad",
+  output = "simulated_dataset.h5ad",
+)
+meta <- list(
+  name = "negative"
+)
+## VIASH END
+
+cat("Reading input files\n")
+input <- anndata::read_h5ad(par$input)
+
+count_matrix <- as.matrix(input$layers[['counts']])
+
+n_rows <- nrow(count_matrix)
+n_cols <- ncol(count_matrix)
+
+random_matrix_uniform <- matrix(runif(n_rows * n_cols), nrow = n_rows, ncol = n_cols)
+rownames(random_matrix_uniform) <- rownames(count_matrix)
+
+cat("Generate outoput file\n")
+output <- anndata::AnnData(
+  layers = list(
+    counts = random_matrix_uniform
+  ),
+  obs = input$obs[c("row", "col")],
+  var = input$var,
+  uns = c(
+    input$uns,
+    list(
+      method_id = meta$name
+    )
+  )
+)
+
+cat("Write output files\n")
+output$write_h5ad(par$output, compression = "gzip")

src/control_methods/positive/config.vsh.yaml

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+__merge__: ../../api/comp_control_method.yaml
+
+name: positive
+label: positive
+summary: A positive control method.
+description: |
+  A positive control method. 
+# references:
+#   doi: 
+
+# info:
+#   documentation_url: https://xzhoulab.github.io/SRTsim
+#   repository_url: https://github.com/xzhoulab/srtsim
+
+resources:
+  - type: r_script
+    path: script.R
+
+engines:
+  - type: docker
+    image: openproblems/base_r:1.0.0
+    setup:
+      - type: r
+        cran: SRTsim
+
+runners:
+  - type: executable
+  - type: nextflow
+    directives:
+      label: [midtime, midmem, midcpu]

src/control_methods/positive/script.R

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+## VIASH START
+par <- list(
+  input = "resources_test/datasets/MOBNEW/dataset_sp.h5ad",
+  output = "simulated_dataset.h5ad"
+)
+meta <- list(
+  name = "positive"
+)
+## VIASH END
+
+cat("Reading input files\n")
+input <- anndata::read_h5ad(par$input)
+
+input$uns$method_id <- meta$name
+
+cat("Write output files\n")
+input$write_h5ad(par$output, compression = "gzip")