preparing for release 3.2

Author: Edwin

manifest

@@ -1,10 +1,10 @@
-# Seurat.Preprocessing  urn:lsid:genepattern.org:module.analysis:00415:2
-#Wed Jul 14 02:04:26 UTC 2021
+# Seurat.Preprocessing  urn:lsid:genepattern.org:module.analysis:00415:3.1
+#Wed Jul 14 04:57:38 UTC 2021
 JVMLevel=
-LSID=urn\:lsid\:genepattern.org\:module.analysis\:00415\:2
-author=Edwin F. Juarez & Jonathan Zamora;UCSD - Mesirov Lab
+LSID=urn\:lsid\:genepattern.org\:module.analysis\:00415\:3.1
+author=Edwin F. Juarez;UCSD - Mesirov Lab
 categories=preprocess & utilities;single-cell
-commandLine=Rscript --no-save --quiet --no-restore <libdir>seurat_preprocess.R --input_rds <input_rds> --min_n_features <min_n_features> --max_n_features <max_n_features> --max_percent_mitochondrial <max_percent_mitochondrial> --norm_method <norm_method> --scale_factor <scale_factor> --feat_sel_method <feat_sel_method> --num_features <num_features> --num_to_label <num_to_label> --vdl_num_dims <vdl_num_dims> --vdhm_num_dims <vdhm_num_dims> --cells <cells> --file_name <file_name>
+commandLine=Rscript --no-save --quiet --no-restore <libdir>seurat_preprocess.R --input_rds <input_rds> --min_n_features <min_n_features> --max_n_features <max_n_features> --max_percent_mitochondrial <max_percent_mitochondrial> --norm_method <norm_method> --scale_factor <scale_factor> --feat_sel_method <feat_sel_method> --num_features <num_features> --num_to_label <num_to_label> --vdl_num_dims <vdl_num_dims> --vdhm_num_dims <vdhm_num_dims> --cells <cells> --file_name <file_name> <keep_scale_data>
 cpuType=any
 description=Seurat preprocessing
 documentationUrl=https\://github.com/genepattern/Seurat.Preprocessing/blob/develop/doc.md
@@ -65,6 +65,19 @@ p13_prefix=
 p13_prefix_when_specified=
 p13_type=java.lang.Integer
 p13_value=
+p14_MODE=
+p14_TYPE=TEXT
+p14_default_value=TRUE
+p14_description=Whether to keep (or prune) scaling data. If you are unsure, leave it as TRUE.
+p14_fileFormat=
+p14_flag=--keep_scale_data
+p14_name=keep_scale_data
+p14_numValues=0..1
+p14_optional=
+p14_prefix=
+p14_prefix_when_specified=
+p14_type=java.lang.String
+p14_value=TRUE\=TRUE;FALSE\=FALSE
 p1_MODE=IN
 p1_TYPE=FILE
 p1_default_value=
@@ -189,4 +202,4 @@ src.repo=https\://github.com/genepattern/Seurat.Preprocessing
 taskDoc=doc.html
 taskType=preprocess & utilities
 userid=edjuaro
-version=Upgrading to Seurat v4.0.3
+version=Upgrading to Seurat 4.0.3

paramgroups.json

@@ -5,8 +5,7 @@
         "hidden": false,
         "parameters": [
             "input_rds",
-            "file_name",
-            "keep_scale_data"
+            "file_name"
         ]
     },
     {
@@ -37,7 +36,8 @@
             "num_to_label",
             "vdl_num_dims",
             "vdhm_num_dims",
-            "cells"
+            "cells",
+            "keep_scale_data"
         ]
     }
-]
+]

prerelease.version

@@ -17,4 +17,4 @@
 #updated before first build
 #Wed, 1 May 2018 15:30:42
 #prerelease version number
-prerelease.number=2
+prerelease.number=1

release.version

@@ -1,3 +1,3 @@
 #update release version number
 #Fri, 20 Nov 2020 01:10:16 -0500
-build.number=2
+build.number=4

run_seurat.sh

@@ -1,4 +1,4 @@
-docker run -v $PWD:/LOCAL -w $PWD/Job_1 -t genepattern/seurat-suite:4.0.3 Rscript --no-save --quiet --slave --no-restore  /LOCAL/src/seurat_preprocess.R\
+docker run -v $PWD:/LOCAL -w /LOCAL/Job_1 -t genepattern/seurat-suite:4.0.3 Rscript --no-save --quiet --slave --no-restore  /LOCAL/src/seurat_preprocess.R\
  --input_rds '/LOCAL/data/test_run.rds' \
  --column_name "percent.mt" --pattern 'MT-'\
  --first_feature 'nFeature_RNA' --second_feature 'nCount_RNA' --third_feature 'percent.mt'\
@@ -8,4 +8,4 @@ docker run -v $PWD:/LOCAL -w $PWD/Job_1 -t genepattern/seurat-suite:4.0.3 Rscrip
  --vdl_num_dims 2\
  --vdhm_num_dims 15 --cells 500\
  --file_name "test_run"\
- --keep_scale_data TRUE
+ --keep_scale_data "TRUE"

src/seurat_preprocess.R

@@ -255,7 +255,7 @@ parser <- add_option(parser, c("--vdhm_num_dims"),type='integer',default=15, hel
 parser <- add_option(parser, c("--cells"),type='integer',default=500, help = "Number of top cells to plot.")
 # ====================================
 #parameter for save_it
-parser <- add_option(parser, c("--keep_scale_data"), type='logical', default=TRUE, help = "Save Scaled Counts for Downstream Analysis.")
+parser <- add_option(parser, c("--keep_scale_data"), type='character', default='TRUE', help = "Save Scaled Counts for Downstream Analysis.")
 parser <- add_option(parser, c("--file_name"),type='character',default='seurat_preprocessed_dataset', help = "Basename of the file to be saved.")
 # ====================================
 
@@ -413,7 +413,7 @@ output_size_list <- append(output_size_list, object.size(pbmc))
 print(object.size(pbmc), units="auto")
 
 
-if (args$keep_scale_data == FALSE) {
+if (args$keep_scale_data == 'FALSE') {
   # Why are we calling Diet Seurat? Read this issue:
   # https://github.com/satijalab/seurat/issues/3892
   print("*************************************")