--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scanpy-read-10x.xml	Wed Apr 03 11:11:38 2019 -0400
@@ -0,0 +1,66 @@
+<?xml version="1.0" encoding="utf-8"?>
+<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>
+  </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 '${var_names}'
+]]></command>
+
+  <inputs>
+    <param name="matrix" type="data" format="txt" label="Expression matrix in sparse matrix format (.mtx)"/>
+    <param name="genes" type="data" format="tsv,tabular" label="Gene table"/>
+    <param name="barcodes" type="data" format="tsv,tabular" label="Barcode/cell table"/>
+    <expand macro="output_object_params"/>
+    <param name="var_names" type="select" label="Attribute used as annotation index">
+      <option value="gene_ids" selected="true">Gene ID</option>
+      <option value="gene_symbols">Gene symbol</option>
+    </param>
+  </inputs>
+
+  <outputs>
+    <data name="output_h5" format="h5" from_work_dir="read_10x.h5" label="${tool.name} on ${on_string}: ${output_format}"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="matrix" value="matrix.mtx"/>
+      <param name="genes" value="genes.tsv"/>
+      <param name="barcodes" value="barcodes.tsv"/>
+      <param name="output_format" value="anndata"/>
+      <output name="output_h5" file="read_10x.h5" ftype="h5" compare="sim_size"/>
+    </test>
+  </tests>
+
+  <help><![CDATA[
+==========================================================
+Read 10x-Genomics-formatted mtx directory (`read_10x_mtx`)
+==========================================================
+
+The mtx directory should contain:
+
+1) Raw expression quantification as a sparse matrix in Matrix Market format, where the each column is a gene and each row is a barcode/cell.
+
+2) A gene table of at least two columns where the first column gives the gene IDs.
+
+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.
+
+
+@HELP@
+
+@VERSION_HISTORY@
+]]></help>
+  <expand macro="citations"/>
+</tool>