Change rds datatype to rdata

ebi-gene-expression-group · Sep 11, 2018 · f4f0d3b · f4f0d3b
1 parent 46aec68
commit f4f0d3b
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Showing 10 changed files with 35 additions and 35 deletions.
diff --git a/tools/seurat_scripts/seurat_create_object.xml b/tools/seurat_scripts/seurat_create_object.xml
@@ -13,17 +13,17 @@ seurat-create-seurat-object.R
 ]]></command>
 
     <inputs>
-        <param name="input" type="data" format="rds" label="RDS object" />
+        <param name="input" type="data" format="rdata" label="RDS object" />
     </inputs>
 
     <outputs>
-        <data name="output" format="rds" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/>
+        <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/>
     </outputs>
 
     <tests>
         <test>
-            <param name="input" ftype="rds" value="deng.rds"/>
-            <output name="output" ftype="rds" value="seurat.rds" compare="sim_size"/>
+            <param name="input" ftype="rdata" value="deng.rds"/>
+            <output name="output" ftype="rdata" value="seurat.rds" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[

diff --git a/tools/seurat_scripts/seurat_filter_cells.xml b/tools/seurat_scripts/seurat_filter_cells.xml
@@ -27,7 +27,7 @@ seurat-filter-cells.R
 ]]></command>
 
     <inputs>
-        <param name="input" type="data" format="rds" label="RDS object" />
+        <param name="input" type="data" format="rdata" label="RDS object" />
         <param name="subset" type="text" label="Subset names" optional="True" help="Default: nUMI">
             <validator type="regex" message="Please only use letters or numbers">^[\(\w\)]+$</validator>
         </param>
@@ -37,13 +37,13 @@ seurat-filter-cells.R
     </inputs>
 
     <outputs>
-        <data name="output" format="rds" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/>
+        <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/>
     </outputs>
 
     <tests>
         <test>
-            <param name="input" ftype="rds" value="seurat.rds"/>
-            <output name="output" ftype="rds" value="out_filter.rds" compare="sim_size"/>
+            <param name="input" ftype="rdata" value="seurat.rds"/>
+            <output name="output" ftype="rdata" value="out_filter.rds" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[

diff --git a/tools/seurat_scripts/seurat_find_clusters.xml b/tools/seurat_scripts/seurat_find_clusters.xml
@@ -14,19 +14,19 @@ seurat-find-clusters.R
 ]]></command>
 
     <inputs>
-        <param name="input" type="data" format="rds" label="RDS object" />       
+        <param name="input" type="data" format="rdata" label="RDS object" />
     </inputs>
 
     <outputs>
-        <data name="output" format="rds" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/>
+        <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/>
         <data name="output_tab" format="tabular" from_work_dir="output_tab" label="${tool.name} on ${on_string}: Seurat RDS"/>
     </outputs>
 
     <tests>
         <!-- Ensure count matrix input works -->
         <test>
-            <param name="input" ftype="rds" value="out_runpca.rds"/>
-            <output name="output" ftype="rds" value="out_findclust.rds" compare="sim_size"/>
+            <param name="input" ftype="rdata" value="out_runpca.rds"/>
+            <output name="output" ftype="rdata" value="out_findclust.rds" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[

diff --git a/tools/seurat_scripts/seurat_find_markers.xml b/tools/seurat_scripts/seurat_find_markers.xml
@@ -13,7 +13,7 @@ seurat-find-markers.R
 ]]></command>
 
     <inputs>
-        <param name="input" type="data" format="rds" label="RDS object" />
+        <param name="input" type="data" format="rdata" label="RDS object" />
     </inputs>
 
     <outputs>
@@ -22,7 +22,7 @@ seurat-find-markers.R
 
     <tests>
         <test>
-            <param name="input" ftype="rds" value="out_runtsne.rds"/>
+            <param name="input" ftype="rdata" value="out_runtsne.rds"/>
             <output name="output" ftype="txt" value="out_findmark.txt"/>
         </test>
     </tests>

diff --git a/tools/seurat_scripts/seurat_find_variable_genes.xml b/tools/seurat_scripts/seurat_find_variable_genes.xml
@@ -32,7 +32,7 @@ seurat-find-variable-genes.R
 ]]></command>
 
     <inputs>
-        <param name="input" type="data" format="rds" label="RDS object" />
+        <param name="input" type="data" format="rdata" label="RDS object" />
         <param name="mean" type="text" optional="True" label="Mean function" />
         <param name="disp" type="float" optional="True" label="Dispersion function" />
         <param name="xlow" type="float" optional="True" label="X-axis low cutoff" />
@@ -42,14 +42,14 @@ seurat-find-variable-genes.R
     </inputs>
 
     <outputs>
-        <data name="output" format="rds" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/>
+        <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/>
         <data name="output_tab" format="tabular" from_work_dir="*.tab" label="${tool.name} on ${on_string}: Variable genes tabular file"/>
     </outputs>
 
     <tests>
         <test>
-            <param name="input" ftype="rds" value="out_norm.rds"/>
-            <output name="output" ftype="rds" value="out_findvar.rds" compare="sim_size"/>
+            <param name="input" ftype="rdata" value="out_norm.rds"/>
+            <output name="output" ftype="rdata" value="out_findvar.rds" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[

diff --git a/tools/seurat_scripts/seurat_macros.xml b/tools/seurat_scripts/seurat_macros.xml
@@ -20,4 +20,4 @@ echo $(R --version | grep version | grep -v GNU)", seurat version" $(R --vanilla
             <citation type="doi">10.1038/nbt.4096</citation>
         </citations>
     </xml>
-</macros>
+</macros>
diff --git a/tools/seurat_scripts/seurat_normalise_data.xml b/tools/seurat_scripts/seurat_normalise_data.xml
@@ -22,7 +22,7 @@ seurat-normalise-data.R
 ]]></command>
 
     <inputs>
-        <param name="input" type="data" format="rds" label="Seurat object" />
+        <param name="input" type="data" format="rdata" label="Seurat object" />
         <param name="norm" type="text" optional="True" label="Normalisation method" />
         <param name="assay" type="text" optional="True" label="Assay type" help="Default: RNA">
             <validator type="regex" message="Please only use letters">^[\(\w\)]+$</validator>
@@ -31,13 +31,13 @@ seurat-normalise-data.R
     </inputs>
 
     <outputs>
-        <data name="output" format="rds" from_work_dir="*.rds" label="${tool.name} on ${on_string}: RDS file"/>
+        <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: RDS file"/>
     </outputs>
 
     <tests>
         <test>
-            <param name="input" ftype="rds" value="seurat.rds"/>
-            <output name="output" ftype="rds" value="out_norm.rds" compare="sim_size"/>
+            <param name="input" ftype="rdata" value="seurat.rds"/>
+            <output name="output" ftype="rdata" value="out_norm.rds" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[

diff --git a/tools/seurat_scripts/seurat_run_pca.xml b/tools/seurat_scripts/seurat_run_pca.xml
@@ -19,21 +19,21 @@ seurat-run-pca.R
 ]]></command>
 
     <inputs>
-        <param name="input" type="data" format="rds" label="RDS object" />
+        <param name="input" type="data" format="rdata" label="RDS object" />
         <param name="pc_genes" type="data" format="tabular, txt" optional="True" label="Genes to scale" help="File of gene names to scale/center. Default is all genes in object." />
     </inputs>
 
     <outputs>
-        <data name="output" format="rds" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/>
+        <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/>
         <data name="output_embed" format="csv" from_work_dir="output_embed" label="${tool.name} on ${on_string}: Seurat Embeddings"/>
         <data name="output_load" format="csv" from_work_dir="output_load" label="${tool.name} on ${on_string}: Seurat Loadings"/>
         <data name="output_sdev" format="csv" from_work_dir="output_sdev" label="${tool.name} on ${on_string}: Seurat Std dev"/>
     </outputs>
 
     <tests>
         <test>
-            <param name="input" ftype="rds" value="out_scale.rds"/>
-            <output name="output" ftype="rds" value="out_runpca.rds" compare="sim_size"/>
+            <param name="input" ftype="rdata" value="out_scale.rds"/>
+            <output name="output" ftype="rdata" value="out_runpca.rds" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[

diff --git a/tools/seurat_scripts/seurat_run_tsne.xml b/tools/seurat_scripts/seurat_run_tsne.xml
@@ -20,19 +20,19 @@ seurat-run-tsne.R
 ]]></command>
 
     <inputs>
-        <param name="input" type="data" format="rds" label="RDS object" />
+        <param name="input" type="data" format="rdata" label="RDS object" />
         <param name="dims_use" type="text" label="Dimensions to use" help="A comma-separated list of the which dimensions to use as input features. Default is 1,10"/>
     </inputs>
 
     <outputs>
-        <data name="output" format="rds" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/>
+        <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/>
         <data name="output_embed" format="csv" from_work_dir="output_embed" label="${tool.name} on ${on_string}: Seurat Embeddings"/>
     </outputs>
 
     <tests>
         <test>
-            <param name="input" ftype="rds" value="out_findclust.rds"/>
-            <output name="output" ftype="rds" value="out_runtsne.rds" compare="sim_size"/>
+            <param name="input" ftype="rdata" value="out_findclust.rds"/>
+            <output name="output" ftype="rdata" value="out_runtsne.rds" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[

diff --git a/tools/seurat_scripts/seurat_scale_data.xml b/tools/seurat_scripts/seurat_scale_data.xml
@@ -18,18 +18,18 @@ seurat-scale-data.R
 ]]></command>
 
     <inputs>
-        <param name="input" type="data" format="rds" label="RDS object" />
+        <param name="input" type="data" format="rdata" label="RDS object" />
         <param name="vars" type="text" optional="True" label="Vars to regress" />
     </inputs>
 
     <outputs>
-        <data name="output" format="rds" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/>
+        <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/>
     </outputs>
 
     <tests>
         <test>
-            <param name="input" ftype="rds" value="out_findvar.rds"/>
-            <output name="output" ftype="rds" value="out_scale.rds" compare="sim_size"/>
+            <param name="input" ftype="rdata" value="out_findvar.rds"/>
+            <output name="output" ftype="rdata" value="out_scale.rds" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[