--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Apr 18 13:18:50 2023 +0000
@@ -0,0 +1,98 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.3.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.01</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">episcanpy</requirement>
+            <requirement type="package" version="1.0.8">bzip2</requirement>
+            <requirement type="package" version="1.11">tabix</requirement>
+            <requirement type="package" version="0.7.5">anndata</requirement>
+            <requirement type="package" version="0.8.3">leidenalg</requirement>
+            <requirement type="package" version="0.8.0">louvain</requirement>
+            <yield />
+        </requirements>
+    </xml>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">episcanpy</xref>
+        </xrefs>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1038/s41467-021-25131-3</citation>
+        </citations>
+    </xml>
+    <xml name="version_command">
+        <version_command><![CDATA[python -c "import episcanpy as esc; print(f'{esc.__version__}')"]]></version_command>
+    </xml>
+    <token name="@CMD@"><![CDATA[
+cp '$adata' 'anndata.h5ad' &&
+cat '$script_file' > '$hidden_output' &&
+python '$script_file' >> '$hidden_output' &&
+touch 'anndata_info.txt' &&
+cat 'anndata_info.txt' @CMD_prettify_stdout@
+    ]]>
+    </token>
+    <token name="@CMD_imports@"><![CDATA[
+import episcanpy as esc
+import pandas as pd
+import numpy as np
+    ]]>
+    </token>
+    <xml name="sanitize_query" token_validinitial="string.printable">
+        <sanitizer>
+            <valid initial="@VALIDINITIAL@">
+                <remove value="&apos;" />
+            </valid>
+       </sanitizer>
+    </xml>
+    <xml name="sanitize_vectors" token_validinitial="string.digits">
+        <sanitizer>
+            <valid initial="@VALIDINITIAL@">
+                <add value=","/>
+            </valid>
+        </sanitizer>
+    </xml>
+    <xml name="inputs_anndata">
+        <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
+    </xml>
+    <token name="@CMD_read_inputs@"><![CDATA[
+adata = esc.read('anndata.h5ad')
+]]>
+    </token>
+    <xml name="inputs_common_advanced">
+        <section name="advanced_common" title="Advanced Options" expanded="false">
+            <param name="show_log" type="boolean" checked="false" label="Output Log?" />
+        </section>
+    </xml>
+    <xml name="anndata_outputs">
+        <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/>
+        <data name="hidden_output" format="txt" label="Log file" hidden="true">
+            <filter>advanced_common['show_log']</filter>
+        </data>
+    </xml>
+    <token name="@CMD_anndata_write_outputs@"><![CDATA[
+adata.write('anndata.h5ad')
+with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
+    print(adata, file=ainfo)
+]]></token>
+    <token name="@CMD_prettify_stdout@"><![CDATA[ | sed -r '1 s|AnnData object with (.+) = (.*)\s*|\1: \2|g' | sed "s|'||g"  | sed -r 's|^\s*(.*):\s(.*)|[\1]\n-    \2|g' | sed 's|, |\n-    |g'
+    ]]></token>
+    <xml name="coverage_params">
+        <param argument="binary" type="boolean" truevalue="True" falsevalue="False" checked="false" 
+            label="Binarized matrix?" help="To reduce computing time, you can specify if the matrix is already binary" />
+        <param argument="log" type="boolean" truevalue="True" falsevalue="False" checked="false"
+            label="Log transform?" />
+        <param argument="threshold" type="float" min="0" value="" label="Minimum number of cells or minimumn number of features to be indicated in the plot"
+            help="For coverage cells, please use min number of features and for coverage features, use min number of cells."/>
+        <param argument="bins" type="integer" min="0" value="50" label="Number of bins in the output histogram plot"/>
+    </xml>
+    <xml name="param_plot_format">
+        <param name="format" type="select" label="Format for saving figures">
+            <option value="png">png</option>
+            <option value="pdf">pdf</option>
+            <option value="svg">svg</option>
+        </param>
+    </xml>
+</macros>