--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Dec 09 17:40:27 2022 +0000
@@ -0,0 +1,65 @@
+<macros>
+    <token name="@VERSION@">0.7</token>
+    <token name="@PROFILE@">21.05</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">cherri</requirement>
+        </requirements>
+    </xml>
+    <macro name="reference_source_conditional">
+        <conditional name="ref_source">
+            <param name="ref_source_selector" type="select" label="Reference genome in FASTA format">
+                <option value="cached">locally cached</option>
+                <option value="history">in your history</option>
+            </param>
+            <when value="cached">
+                <param name="genome_fasta" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
+                    <options from_data_table="all_fasta">
+                        <filter type="sort_by" column="2" />
+                        <validator type="no_options" message="No indices are available." />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="genome_fasta" type="data" format="fasta" label="Select a reference dataset in FASTA format" />
+            </when>
+        </conditional>
+        <param name="chrom_len_file" type="data" format="tabular" label="Two column tabular file containing chromosome lengths" help="Format: 'chrom name' \t 'chrom length'" />        
+    </macro>
+    <token name="@COMMONPARAMS@" ><![CDATA[
+            #if $intarna_param_file: 
+                -p '$intarna_param_file'
+            #end if
+            -c '$context'
+            -st $use_structure
+            -t '$run_time'
+            -me "\${GALAXY_MEMORY_MB_PER_SLOT:-8000}"
+            -j "\${GALAXY_SLOTS:-1}"
+        ]]></token>
+    <xml name="edam_ontology">
+        <edam_topics>
+            <edam_topic>topic_0080</edam_topic>
+            <edam_topic>topic_0081</edam_topic>
+            <edam_topic>topic_0160</edam_topic>
+        </edam_topics>
+        <edam_operations>
+            <edam_operation>operation_2995</edam_operation>
+        </edam_operations>
+    </xml>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">cherri</xref>
+        </xrefs>
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">cherri</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <yield />
+        </citations>
+    </xml>
+</macros>