--- a/scanpy-read-10x.xml	Wed Apr 03 11:11:38 2019 -0400
+++ b/scanpy-read-10x.xml	Mon Sep 16 08:19:16 2019 -0400
@@ -2,24 +2,33 @@
 <tool id="scanpy_read_10x" name="Scanpy Read10x" version="@TOOL_VERSION@+galaxy0">
   <description>into hdf5 object handled by scanpy</description>
   <macros>
-    <import>scanpy_macros.xml</import>
+    <import>scanpy_macros2.xml</import>
   </macros>
   <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
 ln -s '${matrix}' matrix.mtx &&
 ln -s '${genes}' genes.tsv &&
 ln -s '${barcodes}' barcodes.tsv &&
-PYTHONIOENCODING=utf-8 scanpy-read-10x.py
-    -d ./
-    -o read_10x.h5
-    -F '${output_format}'
-    -v '${var_names}'
+PYTHONIOENCODING=utf-8 scanpy-read-10x
+    --input-10x-mtx ./
+    --var-names '${var_names}'
+#if $cell_meta:
+    --extra-obs '${cell_meta}'
+#end if
+#if $gene_meta:
+    --extra-var '${gene_meta}'
+#end if
+    @OUTPUT_OPTS@
 ]]></command>
 
   <inputs>
     <param name="matrix" type="data" format="txt" label="Expression matrix in sparse matrix format (.mtx)"/>
     <param name="genes" type="data" format="tsv,tabular" label="Gene table"/>
     <param name="barcodes" type="data" format="tsv,tabular" label="Barcode/cell table"/>
+    <param name="cell_meta" type="data" format="tsv,tabular" label="Cell metadata table" optional="true"
+           help="Requires a header row and index column that matches the barcode/cell table"/>
+    <param name="gene_meta" type="data" format="tsv,tabular" label="Gene metadata table" optional="true"
+           help="Requires a header row and index column that matches the gene table"/>
     <expand macro="output_object_params"/>
     <param name="var_names" type="select" label="Attribute used as annotation index">
       <option value="gene_ids" selected="true">Gene ID</option>
@@ -28,7 +37,7 @@
   </inputs>
 
   <outputs>
-    <data name="output_h5" format="h5" from_work_dir="read_10x.h5" label="${tool.name} on ${on_string}: ${output_format}"/>
+    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: ${output_format}"/>
   </outputs>
 
   <tests>
@@ -36,15 +45,16 @@
       <param name="matrix" value="matrix.mtx"/>
       <param name="genes" value="genes.tsv"/>
       <param name="barcodes" value="barcodes.tsv"/>
+      <!-- <param name="cell_meta" value=""/> -->
       <param name="output_format" value="anndata"/>
-      <output name="output_h5" file="read_10x.h5" ftype="h5" compare="sim_size"/>
+      <output name="output_h5" file="output.h5" ftype="h5" compare="sim_size"/>
     </test>
   </tests>
 
   <help><![CDATA[
-==========================================================
-Read 10x-Genomics-formatted mtx directory (`read_10x_mtx`)
-==========================================================
+=================================================================
+Read 10x-Genomics-formatted mtx directory (`scanpy.read_10x_mtx`)
+=================================================================
 
 The mtx directory should contain:
 
@@ -54,8 +64,9 @@
 
 3) A barcode/cell table of at least one column giving the barcode/cell IDs.
 
-The above-mentioned files can be obtained by running `EBI SCXA Data Retrieval`
-with a dataset accession.
+The above-mentioned files can be obtained by running `EBI SCXA Data Retrieval` with a dataset accession or `Human Cell Atlas Matrix Downloader` with a project name/label/UUID.
+
+Additionally, cell and/or gene metadata table can be provided as tab-separated text with a header row and an index column that matches the respective barcode/cell and/or gene table.
 
 
 @HELP@