diff anndata_operations.xml @ 11:f0a29f4b9be9 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit e2ec0706fd62528e5198e3c050d91ab0ee6cd4da"

--- a/anndata_operations.xml	Thu Jun 11 13:07:33 2020 -0400
+++ b/anndata_operations.xml	Fri Jun 12 09:19:22 2020 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="anndata_ops" name="AnnData Operations" version="0.0.3+galaxy0" profile="@PROFILE@">
+<tool id="anndata_ops" name="AnnData Operations" version="0.0.3+galaxy1" profile="@PROFILE@">
   <description>modifies metadata and flags genes</description>
   <macros>
     <import>scanpy_macros2.xml</import>
@@ -36,6 +36,10 @@
 
 adata = sc.read('input.h5')
 
+#if $copy_adata_to_raw:
+adata.raw = adata
+#end if
+
 gene_name = '${gene_symbols_field}'
 qc_vars = list()
 
@@ -128,6 +132,7 @@
   <inputs>
     <param name="input_obj_file" argument="input-object-file" type="data" format="h5,h5ad" label="Input object in hdf5 AnnData format"/>
     <expand macro="output_object_params_no_loom"/>
+    <param name="copy_adata_to_raw" type="boolean" label="Copy AnnData to .raw" help="If activated, it will do 'adata.raw = adata'" checked="false"/>
     <repeat name="modifications" title="Change field names in AnnData observations" min="0">
       <param name="from_obs" type="text" label="Original name" help="Name in observations that you want to change">
         <sanitizer>