# HG changeset patch
# User ebi-gxa
# Date 1696151225 0
# Node ID 412e62cb6cf7ed530d728abdf84f386e9c8790a7
# Parent 52ccdd3fb5e830e2f1f954b41951b73c0b56203b
planemo upload commit 34c30124158749b9eef51d5f323b608a503e7940
diff -r 52ccdd3fb5e8 -r 412e62cb6cf7 extra/macro_mapper_seurat.yaml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/extra/macro_mapper_seurat.yaml Sun Oct 01 09:07:05 2023 +0000
@@ -0,0 +1,90 @@
+---
+- option_group:
+ - input-object-file
+ - input-format
+ pre_command_macros:
+ - INPUT_OBJ_PREAMBLE
+ post_command_macros:
+ - INPUT_OBJECT
+ input_declaration_macros:
+ - input_object_params
+- option_group:
+ - output-object-file
+ - output-format
+ post_command_macros:
+ - OUTPUT_OBJECT
+ input_declaration_macros:
+ - output_object_params
+ output_declaration_macros:
+ - output_files
+- option_group:
+ - input-object-files
+ - input-format
+ pre_command_macros:
+ - INPUT_OBJS_PREAMBLE
+ post_command_macros:
+ - INPUT_OBJECTS
+ input_declaration_macros:
+ - input_object_params:
+ multiple: true
+- option_group:
+ - reference-object-files
+ - reference-format
+ pre_command_macros:
+ - REFERENCE_OBJS_PREAMBLE
+ post_command_macros:
+ - REFERENCE_OBJECTS
+ input_declaration_macros:
+ - input_object_params:
+ varname: reference
+ multiple: true
+ optional: true
+- option_group:
+ - reference-object-file
+ - reference-format
+ pre_command_macros:
+ - REFERENCE_OBJ_PREAMBLE
+ post_command_macros:
+ - REFERENCE_OBJECT
+ input_declaration_macros:
+ - input_object_params:
+ varname: reference
+- option_group:
+ - anchors-object-file
+ - anchors-format
+ pre_command_macros:
+ - ANCHORS_OBJ_PREAMBLE
+ post_command_macros:
+ - ANCHORS_OBJECT
+ input_declaration_macros:
+ - input_object_params:
+ varname: anchors
+- option_group:
+ - query-object-file
+ - query-format
+ pre_command_macros:
+ - QUERY_OBJ_PREAMBLE
+ post_command_macros:
+ - QUERY_OBJECT
+ input_declaration_macros:
+ - input_object_params:
+ varname: query
+- option_group:
+ - plot-out
+ post_command_macros:
+ - OUTPUT_PLOT
+ output_declaration_macros:
+ - plot_output_files_format:
+ format: png
+ - plot_output_files_format:
+ format: pdf
+ - plot_output_files_format:
+ format: eps
+ - plot_output_files_format:
+ format: jpg
+ - plot_output_files_format:
+ format: ps
+ - plot_output_files_format:
+ format: tiff
+ - plot_output_files_format:
+ format: svg
diff -r 52ccdd3fb5e8 -r 412e62cb6cf7 get_test_data.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/get_test_data.sh Sun Oct 01 09:07:05 2023 +0000
@@ -0,0 +1,77 @@
+#!/usr/bin/env bash
+
+BASENAME_FILE='E-MTAB-6077-3k_features_90_cells'
+
+MTX_LINK='https://drive.google.com/uc?export=download&id=1-1ejn7scP80xsbrG0FtWzsozjg0hhc23'
+RDS_LINK='https://drive.google.com/uc?export=download&id=1KW_GX6xznSUpWRWUykpNaSbAhyClf7_n'
+NORM_LINK='https://drive.google.com/uc?export=download&id=1mvo3ENkBvEAOyWG6ejApzQTPDLX5yBKU'
+FVG_LINK='https://drive.google.com/uc?export=download&id=13Fhruuj-vEEo1WM138ahtAYqfHc7LsaZ'
+SCALED_LINK='https://drive.google.com/uc?export=download&id=18TK8us235LWNajarWDBAtASUXMYAxvw0'
+PCA_LINK='https://drive.google.com/uc?export=download&id=1gf3BTB4dygDsom1TzjsBfgZnZepcoG5c'
+NEIGHBOURS_LINK='https://drive.google.com/uc?export=download&id=1N2lHoKRBZ7pmAYGfghLWB9KUrLA5WoNX'
+CLUSTERS_LINK='https://drive.google.com/uc?export=download&id=1HWxZWHbNUNo4z__9PhhL_CJOLzec_ETa'
+TSNE_LINK='https://drive.google.com/uc?export=download&id=1qsvMr_GkCSp1dyTJt1BZ6cElJwFFX2zO'
+MARKERS_LINK='https://drive.google.com/uc?export=download&id=18OmWNc7mF-4pzH6DQkPp1eKunN4BfvxD'
+
+LOOM_LINK='https://drive.google.com/uc?export=download&id=1qNk5cg8hJG3Nv1ljTKmUEnxTOf11EEZX'
+H5AD_LINK='https://drive.google.com/uc?export=download&id=1YpE0H_t_dkh17P-WBhPijKvRiGP0BlBz'
+
+H5AD_SC182_LINK='https://drive.google.com/uc?export=download&id=16PUJ2KAkXT8F1UkfqU-9LWoOJUkUG1rp'
+SCE_LINK='https://drive.google.com/uc?export=download&id=1UKdyf3M01uAt7oBg93JfmRvNVB_jlUKe'
+
+# Seurat v4 exclusives
+IFNB_BASE_FILE='ifnb_'
+
+IFNB_CTRL_INT_LINK='https://drive.google.com/uc?export=download&id=15E_MLz-UclJYInNaA7YKLhLo5W-qlykL'
+IFNB_STIM_INT_LINK='https://drive.google.com/uc?export=download&id=14iKgCJGPk16dEmpJJF-Gp_lBDcOdo-54'
+
+## Classify and UMAP mapping
+CLASSIFY_QUERY_LINK='https://drive.google.com/uc?export=download&id=1RFsHa_1EFD_n-19JH_cHGqxwO66QdmXN'
+CLASSIFY_RESULTS_ANCHORS_OBJECT_LINK='https://drive.google.com/uc?export=download&id=1Xtv4K_CxIU1cJ8RjJ7NTvzLQkLvc8a3i'
+# UMAP_RESULT_OBJECT_LINK='https://oc.ebi.ac.uk/s/k4MdM07y9DAnurp/download'
+UMAP_RESULT_OBJECT_LINK='https://oc.ebi.ac.uk/s/D1z4z2ef1e3dyc3/download'
+
+
+function get_data {
+ local link=$1
+ local fname=$2
+
+ if [ ! -f $fname ]; then
+ echo "$fname not available locally, downloading.."
+ wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link
+ fi
+}
+
+# get matrix data
+mkdir -p test-data
+pushd test-data
+get_data $MTX_LINK mtx.zip
+unzip mtx.zip
+rm -f mtx.zip
+
+get_data $RDS_LINK $BASENAME_FILE".rds"
+get_data $NORM_LINK $BASENAME_FILE"-normalised.rds"
+get_data $FVG_LINK $BASENAME_FILE"-fvg.rds"
+get_data $SCALED_LINK $BASENAME_FILE"-scaled.rds"
+get_data $PCA_LINK $BASENAME_FILE"-pca.rds"
+get_data $NEIGHBOURS_LINK $BASENAME_FILE"-neighbours.rds"
+get_data $CLUSTERS_LINK $BASENAME_FILE"-clusters.rds"
+get_data $TSNE_LINK $BASENAME_FILE"-tsne.rds"
+get_data $MARKERS_LINK $BASENAME_FILE"-markers.csv.zip"
+
+unzip $BASENAME_FILE"-markers.csv.zip"
+rm -f $BASENAME_FILE"-markers.csv.zip"
+
+get_data $LOOM_LINK $BASENAME_FILE"_loom.h5"
+get_data $SCE_LINK $BASENAME_FILE"_sce.rds"
+get_data $H5AD_LINK $BASENAME_FILE".h5ad"
+
+get_data $H5AD_SC182_LINK $BASENAME_FILE"_sc182.h5ad"
+
+get_data $IFNB_CTRL_INT_LINK $IFNB_BASE_FILE"ctrl_norm_fvg.rds"
+get_data $IFNB_STIM_INT_LINK $IFNB_BASE_FILE"stim_norm_fvg.rds"
+
+get_data $CLASSIFY_QUERY_LINK "Classify_query.rds"
+get_data $CLASSIFY_RESULTS_ANCHORS_OBJECT_LINK "Classify_anchors.rds"
+get_data $UMAP_RESULT_OBJECT_LINK "UMAP_result_integrated.rds"
+
diff -r 52ccdd3fb5e8 -r 412e62cb6cf7 seurat_macros.xml
--- a/seurat_macros.xml Thu Apr 16 09:34:07 2020 +0000
+++ b/seurat_macros.xml Sun Oct 01 09:07:05 2023 +0000
@@ -1,7 +1,7 @@
- 0.0.6
- 3.1.1
+ 4.0.0
+ 4.0.4
seurat-scripts
@@ -13,44 +13,237 @@
]]>
-
-
-
+
+
+
+
-
+
-
+
-
+
-
+
+
+
+
+
+ #if $input.format == 'loom'
+ ln -s '$input.loom_file' input.loom;
+ #else if $input.format == 'h5seurat'
+ ln -s '$input.h5seurat_file' input.h5seurat;
+ #else if $input.format == 'anndata'
+ ## it complains when using links for AnnData...
+ cp '$input.anndata_file' input.h5ad;
+ #end if
+
+
#if $input.format == "anndata"
- --input-object-file '$input.anndata_file' --input-format anndata
+ --input-object-file input.h5ad --input-format anndata
#else if $input.format == "loom"
- --input-object-file '$input.loom_file' --input-format loom
+ --input-object-file input.loom --input-format loom
#else if $input.format == "rds_seurat"
--input-object-file '$input.rds_seurat_file' --input-format seurat
#else if $input.format == "rds_sce"
--input-object-file '$input.rds_sce_file' --input-format singlecellexperiment
+ #else if $input.format == "h5seurat"
+ --input-object-file input.h5seurat --input-format h5seurat
+ #end if
+
+
+
+ #if $query.format == 'loom'
+ ln -s '$query.loom_file' query.loom;
+ #else if $query.format == 'h5seurat'
+ ln -s '$query.h5seurat_file' query.h5seurat;
+ #else if $query.format == 'anndata'
+ ## it complains when using links for AnnData...
+ cp '$query.anndata_file' query.h5ad;
+ #end if
+
+
+
+ #if $query.format == "anndata"
+ --query-object-file query.h5ad --query-format anndata
+ #else if $query.format == "loom"
+ --query-object-file query.loom --query-format loom
+ #else if $query.format == "rds_seurat"
+ --query-object-file '$query.rds_seurat_file' --query-format seurat
+ #else if $query.format == "rds_sce"
+ --query-object-file '$query.rds_sce_file' --query-format singlecellexperiment
+ #else if $query.format == "h5seurat"
+ --query-object-file query.h5seurat --query-format h5seurat
+ #end if
+
+
+
+ #if $anchors.format == 'loom'
+ ln -s '$anchors.loom_file' anchors.loom;
+ #else if $anchors.format == 'h5seurat'
+ ln -s '$anchors.h5seurat_file' anchors.h5seurat;
+ #else if $anchors.format == 'anndata'
+ ## it complains when using links for AnnData...
+ cp '$anchors.anndata_file' anchors.h5ad;
+ #end if
+
+
+
+ #if $anchors.format == "anndata"
+ --anchors-object-file anchors.h5ad --anchors-format anndata
+ #else if $anchors.format == "loom"
+ --anchors-object-file anchors.loom --anchors-format loom
+ #else if $anchors.format == "rds_seurat"
+ --anchors-object-file '$anchors.rds_seurat_file' --anchors-format seurat
+ #else if $anchors.format == "rds_sce"
+ --anchors-object-file '$anchors.rds_sce_file' --anchors-format singlecellexperiment
+ #else if $anchors.format == "h5seurat"
+ --anchors-object-file anchors.h5seurat --anchors-format h5seurat
+ #end if
+
+
+
+ #if $reference.format == 'loom'
+ ln -s '$reference.loom_file' reference.loom;
+ #else if $reference.format == 'h5seurat'
+ ln -s '$reference.h5seurat_file' reference.h5seurat;
+ #else if $reference.format == 'anndata'
+ ## it complains when using links for AnnData...
+ cp '$reference.anndata_file' reference.h5ad;
+ #end if
+
+
+
+ #if $reference.format == "anndata"
+ --reference-object-file reference.h5ad --reference-format anndata
+ #else if $reference.format == "loom"
+ --reference-object-file reference.loom --reference-format loom
+ #else if $reference.format == "rds_seurat"
+ --reference-object-file '$reference.rds_seurat_file' --reference-format seurat
+ #else if $reference.format == "rds_sce"
+ --reference-object-file '$reference.rds_sce_file' --reference-format singlecellexperiment
+ #else if $reference.format == "h5seurat"
+ --reference-object-file reference.h5seurat --reference-format h5seurat
+ #end if
+
+
+
+ #if $input.format == 'loom'
+ #for $i, $fh in enumerate($input.loom_file):
+ ln -s '$fh' input.${i}.loom;
+ #end for
+ #else if $input.format == 'h5seurat'
+ #for $i, $fh in enumerate($input.h5seurat_file):
+ ln -s '$fh' input.${i}.h5seurat;
+ #end for
+ #else if $input.format == 'anndata'
+ ## it complains when using links for AnnData...
+ #for $i, $fh in enumerate($input.anndata_file):
+ cp '$fh' input.${i}.h5ad;
+ #end for
+ #end if
+
+
+
+ #if $input.format == "anndata"
+ --input-object-files
+ #set file_array = [ "input."+str($i)+".h5ad" for $i, $fh in enumerate($input.anndata_file)]
+ #set files = ",".join($file_array)
+ ${files}
+ --input-format anndata
+ #else if $input.format == "loom"
+ --input-object-files
+ #set file_array = [ "input."+str($i)+".loom" for $i, $fh in enumerate($input.loom_file)]
+ #set files = ",".join($file_array)
+ ${files}
+ --input-format loom
+ #else if $input.format == "rds_seurat"
+ --input-object-files
+ #set file_array = $input.rds_seurat_file
+ #set files = ",".join([ str($fh) for $fh in $file_array ])
+ ${files}
+ --input-format seurat
+ #else if $input.format == "rds_sce"
+ --input-object-files
+ #set file_array = $input.rds_sce_file
+ #set files = ",".join([ str($fh) for $fh in $file_array ])
+ ${files}
+ --input-format singlecellexperiment
+ #else if $input.format == "h5seurat"
+ --input-object-files
+ #set file_array = [ "input."+str($i)+".h5seurat" for $i, $fh in enumerate($input.h5seurat)]
+ #set files = ",".join($file_array)
+ ${files}
+ --input-format h5seurat
+ #end if
+
+
+
+ #if $reference.format == 'loom'
+ #for $i, $fh in enumerate($reference.loom_file):
+ ln -s '$fh' reference.${i}.loom;
+ #end for
+ #else if $reference.format == 'h5seurat'
+ #for $i, $fh in enumerate($reference.h5seurat_file):
+ ln -s '$fh' reference.${i}.h5seurat;
+ #end for
+ #else if $reference.format == 'anndata'
+ ## it complains when using links for AnnData...
+ #for $i, $fh in enumerate($reference.anndata_file):
+ cp '$fh' reference.${i}.h5ad;
+ #end for
+ #end if
+
+
+
+ #if $reference.format == "anndata" and $reference.anndata_file:
+ --reference-object-files
+ #set file_array = [ "reference."+str($i)+".h5ad" for $i, $fh in enumerate($reference.anndata_file)]
+ #set files = ",".join($file_array)
+ ${files}
+ --reference-format anndata
+ #else if $reference.format == "loom" and $reference.loom_file:
+ --reference-object-files
+ #set file_array = [ "reference."+str($i)+".loom" for $i, $fh in enumerate($reference.loom_file)]
+ #set files = ",".join($file_array)
+ ${files}
+ --reference-format loom
+ #else if $reference.format == "rds_seurat" and $reference.rds_seurat_file:
+ --reference-object-files
+ #set files = ",".join([ str($fh) for $fh in $reference.rds_seurat_file ])
+ ${files}
+ --reference-format seurat
+ #else if $reference.format == "rds_sce" and $reference.rds_sce_file:
+ --reference-object-files
+ #set files = ",".join([ str($fh) for $fh in $reference.rds_sce_file ])
+ ${files}
+ --reference-format singlecellexperiment
+ #else if $reference.format == "h5seurat" and $reference.h5seurat:
+ --reference-object-files
+ #set file_array = [ "reference."+str($i)+".h5seurat" for $i, $fh in enumerate($reference.h5seurat)]
+ #set files = ",".join($file_array)
+ ${files}
+ --reference-format h5seurat
#end if
-
+
+
@@ -63,6 +256,9 @@
format == 'rds_seurat'
+
+ format == 'anndata'
+
format == 'rds_sce'
@@ -80,6 +276,30 @@
#end if
+
+
+ plot_format == '@FORMAT@'
+
+
+
+
+ #if $plot_format == "png"
+ --plot-out '$plot_out_png'
+ #else if $plot_format == "pdf"
+ --plot-out '$plot_out_pdf'
+ #else if $plot_format == "eps"
+ --plot-out '$plot_out_eps'
+ #else if $plot_format == "ps"
+ --plot-out '$plot_out_ps'
+ #else if $plot_format == "jpg"
+ --plot-out '$plot_out_jpg'
+ #else if $plot_format == "tiff"
+ --plot-out '$plot_out_tiff'
+ #else if $plot_format == "svg"
+ --plot-out '$plot_out_svg'
+ #end if
+
+
@@ -96,20 +316,28 @@
+ 10.1038/s41592-021-01102-w
10.1038/nbt.4096
@misc{r-seurat-scripts.git,
@@ -121,7 +349,6 @@
url = {https://github.com/ebi-gene-expression-group/r-seurat-scripts.git},
}
- 10.1101/2020.04.08.032698
diff -r 52ccdd3fb5e8 -r 412e62cb6cf7 seurat_scale_data.xml
--- a/seurat_scale_data.xml Thu Apr 16 09:34:07 2020 +0000
+++ b/seurat_scale_data.xml Sun Oct 01 09:07:05 2023 +0000
@@ -1,4 +1,4 @@
-
+
scale and center genes
seurat_macros.xml
@@ -70,8 +70,14 @@
-
-
+
+
+
+