diff --git a/.codeocean/app-panel.json b/.codeocean/app-panel.json index 5e79769..4d81488 100644 --- a/.codeocean/app-panel.json +++ b/.codeocean/app-panel.json @@ -16,21 +16,36 @@ "id": "7Rr6IxOMDucKMImp", "name": "Input Data Parameters", "description": "Options for defining input data", - "icon": "📁" + "icon": "\ud83d\udcc1" }, { "id": "EzTg1ivlFDHEy9PI", "name": "Basic", - "icon": "📂" + "icon": "\ud83d\udcc2" }, { "id": "FvI4Z2eb9sjL47Jt", "name": "Advanced", "description": "Advanced parameters", - "icon": "📂" + "icon": "\ud83d\udcc2" } ], "parameters": [ + { + "id": "qsXhqvyKgDh3Vz8u", + "category": "EzTg1ivlFDHEy9PI", + "name": "Count type", + "param_name": "count_type", + "description": "Counts slot name to use for differential expression (e.g., filt)", + "type": "list", + "value_type": "string", + "default_value": "filt", + "extra_data": [ + "raw", + "clean", + "filt" + ] + }, { "id": "73xRrg0JvDvhEkPN", "category": "EzTg1ivlFDHEy9PI", @@ -65,16 +80,6 @@ "default_value": "Group,Batch", "required": true }, - { - "id": "qsXhqvyKgDh3Vz8u", - "category": "FvI4Z2eb9sjL47Jt", - "name": "Count type", - "param_name": "count_type", - "description": "Counts slot name to use for differential expression (e.g., filt)", - "type": "text", - "value_type": "string", - "default_value": "filt" - }, { "id": "WoZUI91NYysibcVj", "category": "FvI4Z2eb9sjL47Jt", @@ -117,9 +122,13 @@ "name": "Input in log counts", "param_name": "input_in_log_counts", "description": "Set TRUE if counts are already log2-transformed", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "FALSE" + "default_value": "FALSE", + "extra_data": [ + "TRUE", + "FALSE" + ] }, { "id": "yxhLfINFuSTTS3Fj", @@ -127,19 +136,33 @@ "name": "Return mean and sd", "param_name": "return_mean_and_sd", "description": "Return group means and standard deviations in addition to DE estimates", - "type": "text", + "type": "list", "value_type": "string", - "default_value": "FALSE" + "default_value": "FALSE", + "extra_data": [ + "TRUE", + "FALSE" + ] }, { "id": "Uq2LuAF8ff8pzM9e", "category": "FvI4Z2eb9sjL47Jt", "name": "voom normalization method", "param_name": "voom_normalization_method", - "description": "Normalization method passed to limma::voom", - "type": "text", + "description": "Normalization method for differential expression. edgeR methods are applied with calcNormFactors before voom; limma methods are passed to voom normalize. limma options: quantile, scale, cyclicloess, none. edgeR options: TMM, TMMwzp, RLE, upperquartile.", + "type": "list", "value_type": "string", - "default_value": "quantile" + "default_value": "quantile", + "extra_data": [ + "quantile", + "scale", + "cyclicloess", + "none", + "TMM", + "TMMwzp", + "RLE", + "upperquartile" + ] } ], "results": [ @@ -147,4 +170,4 @@ "file_name": "figures/diff/mean-variance.png" } ] -} \ No newline at end of file +} diff --git a/CHANGELOG.md b/CHANGELOG.md index c042385..75d9176 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,9 @@ # Code Ocean capsule - MOSuite - differential expression analysis +## Development version + +- Improved the Code Ocean parameter UI for the diff counts capsule (#3, @phoman14). + ## v3.0 - The MOSuite package is now available in `code/MOSuite`. (#2) @@ -17,4 +21,4 @@ - Initial release. - Uses MOSuite v0.2.1-dev docker image. - `8f9bdf7` \ No newline at end of file + `8f9bdf7`