fix core and inputs from zenodo

galaxyproject · Jan 12, 2025 · ed2ea56 · ed2ea56
1 parent 31cdfa7
commit ed2ea56
Show file tree

Hide file tree

Showing 2 changed files with 11 additions and 9 deletions.
diff --git a/tools/spacexr/spacexr_cside.xml b/tools/spacexr/spacexr_cside.xml
@@ -8,6 +8,7 @@
         <requirement type="package" version="3.5.1">r-ggplot2</requirement>
     </expand>
     <command detect_errors="exit_code"><![CDATA[
+        export GALAXY_SLOTS=2 &&
         mkdir -p 'inputs' 'results' 'logs' 'figures' &&
         ln -s '$rctd' 'inputs/rctd.rds' &&
         touch 'results/cside_script.R' &&
@@ -57,6 +58,7 @@ if (is.na(cores) || !nzchar(cores)) {
     cores = 1
 }
 myRCTD@config[["max_cores"]] <- as.numeric(cores)
+print(paste("Using", cores, "cores"))
 
 # CSIDE
 #if str($type.de_type) == 'non_parametric':
@@ -209,7 +211,7 @@ saveRDS(myRCTD, file = 'results/cside_results.rds')
     <tests>
         <!-- test non_parametric -->
         <test expect_num_outputs="2">
-            <param name="rctd" value="myRCTD_merfish.rds"/>
+            <param name="rctd" location="https://zenodo.org/records/14633442/files/myRCTD_merfish.rds"/>
             <param name="de_type" value="non_parametric"/>
             <param name="cell_types" value="Astrocytes"/>
             <param name="cell_type_threshold" value="10"/>
@@ -238,7 +240,7 @@ saveRDS(myRCTD, file = 'results/cside_results.rds')
         </test>
         <!-- test fig and rds -->
         <test expect_num_outputs="6">
-            <param name="rctd" value="myRCTD_merfish.rds"/>
+            <param name="rctd" location="https://zenodo.org/records/14633442/files/myRCTD_merfish.rds"/>
             <param name="de_type" value="non_parametric"/>
             <param name="cell_types" value="Astrocytes"/>
             <param name="cell_type_threshold" value="10"/>
@@ -277,7 +279,7 @@ saveRDS(myRCTD, file = 'results/cside_results.rds')
         </test>
         <!-- test point_density -->
         <test expect_num_outputs="2">
-            <param name="rctd" value="myRCTD_merfish.rds"/>
+            <param name="rctd" location="https://zenodo.org/records/14633442/files/myRCTD_merfish.rds"/>
             <param name="de_type" value="point_density"/>
             <param name="pathologic_barcode" value="f4e9c023\-f3db\-4f6d\-9212\-72b4dc77a3e3"/>
             <param name="cell_types" value="Astrocytes"/>
@@ -306,7 +308,7 @@ saveRDS(myRCTD, file = 'results/cside_results.rds')
         </test>
         <!-- test cell2cell -->
         <test expect_num_outputs="2">
-            <param name="rctd" value="myRCTD_merfish.rds"/>
+            <param name="rctd" location="https://zenodo.org/records/14633442/files/myRCTD_merfish.rds"/>
             <param name="de_type" value="cell2cell"/>
             <param name="cell_type" value="Excitatory"/>
             <param name="cell_types" value="Astrocytes"/>
@@ -336,7 +338,7 @@ saveRDS(myRCTD, file = 'results/cside_results.rds')
         </test>
         <!-- test XY -->
         <test expect_num_outputs="2">
-            <param name="rctd" value="myRCTD_merfish.rds"/>
+            <param name="rctd" location="https://zenodo.org/records/14633442/files/myRCTD_merfish.rds"/>
             <param name="de_type" value="XY"/>
             <param name="lim" value="2000"/>
             <param name="xy" value="X"/>
@@ -366,7 +368,7 @@ saveRDS(myRCTD, file = 'results/cside_results.rds')
         </test>
         <!-- test custom -->
         <test expect_num_outputs="2">
-            <param name="rctd" value="myRCTD_merfish.rds"/>
+            <param name="rctd" location="https://zenodo.org/records/14633442/files/myRCTD_merfish.rds"/>
             <param name="de_type" value="custom"/>
             <param name="pathologic_barcode" value="f4e9c023-f3db-4f6d-9212-72b4dc77a3e3"/>
             <repeat name="region">

diff --git a/tools/spacexr/spacexr_rctd.xml b/tools/spacexr/spacexr_rctd.xml
@@ -259,7 +259,7 @@ saveRDS(myRCTD, file = 'results/rctd_results.rds')
     </outputs>
     <tests>
         <test expect_num_outputs="4">
-            <param name="sc_count" value="sc_count.tabular"/>
+            <param name="sc_count" location="https://zenodo.org/records/14633442/files/sc_count.tabular"/>
             <param name="metadata" value="metadata.tabular"/>
             <param name="sc_umi_input" value="True"/>
             <param name="st_count" value="st_count.tabular"/>
@@ -293,7 +293,7 @@ saveRDS(myRCTD, file = 'results/rctd_results.rds')
             </output>
         </test>
         <test expect_num_outputs="3">
-            <param name="sc_count" value="sc_count.tabular"/>
+            <param name="sc_count" location="https://zenodo.org/records/14633442/files/sc_count.tabular"/>
             <param name="metadata" value="metadata.tabular"/>
             <param name="sc_umi_input" value="False"/>
             <param name="st_count" value="st_count.tabular"/>
@@ -316,7 +316,7 @@ saveRDS(myRCTD, file = 'results/rctd_results.rds')
             </output>
         </test>
         <test expect_num_outputs="4">
-            <param name="sc_count" value="sc_count.tabular"/>
+            <param name="sc_count" location="https://zenodo.org/records/14633442/files/sc_count.tabular"/>
             <param name="metadata" value="metadata.tabular"/>
             <param name="sc_umi_input" value="False"/>
             <param name="st_count" value="st_count.tabular"/>