--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed May 29 14:25:02 2024 +0000
@@ -0,0 +1,85 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.0.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@profile@">22.05</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">cosg</requirement>
+            <requirement type="package" version="1.9.8">scanpy</requirement>
+            <requirement type="package" version="1.5.3">pandas</requirement>
+            <requirement type="package" version="3.7">matplotlib</requirement>
+            <requirement type="package" version="0.12.2">seaborn</requirement>
+            <yield />
+        </requirements>
+    </xml>
+    <xml name="creators">
+        <creator>
+            <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
+        </creator>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bib/bbab579</citation>
+            <citation type="doi">10.1093/gigascience/giaa102</citation>
+        </citations>
+    </xml>
+    <xml name="version_command">
+        <version_command><![CDATA[python -c "import cosg;import importlib.metadata;print('%s' % importlib.metadata.version('cosg'))"]]></version_command>
+    </xml>
+    <token name="@CMD@"><![CDATA[
+cp '$adata' 'anndata.h5ad' &&
+cat '$script_file' > '$hidden_output' &&
+python '$script_file' >> '$hidden_output' &&
+ls . >> '$hidden_output' &&
+touch 'anndata_info.txt' &&
+cat 'anndata_info.txt' @CMD_prettify_stdout@
+    ]]>
+    </token>
+    <token name="@CMD_imports@"><![CDATA[
+import scanpy as sc
+import pandas as pd
+import numpy as np
+import cosg
+    ]]>
+    </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 = sc.read_h5ad('anndata.h5ad')
+]]>
+    </token>
+    <xml name="inputs_common_advanced">
+        <section name="advanced_common" title="Advanced Output 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} on ${on_string}: Annotated data matrix"/>
+        <data name="hidden_output" format="txt" label="Log file" >
+            <filter>advanced_common['show_log']</filter>
+        </data>
+    </xml>
+    <token name="@CMD_anndata_write_outputs@"><![CDATA[
+adata.write_h5ad('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>
+</macros>