--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Jan 20 19:49:40 2021 +0000
@@ -0,0 +1,66 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@TOOL_VERSION@">1.0.11</token>
+    <token name="@VERSION_SUFFIX@">0</token>    
+    <token name="@PROFILE@">20.01</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">jasminesv</requirement>
+        </requirements>
+    </xml>
+    <xml name="version_command">
+        <version_command>jasmine</version_command>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">@online{jasmine,
+              author = {Melanie Kirsche},
+              title = {jasmine},
+              year = 2021,
+              url = {https://github.com/mkirsche/Jasmine},
+              urldate = {2021-01-13}
+            }</citation>
+        </citations>
+    </xml>
+    <!--
+        Command
+    -->
+    <token name="@REF_FASTA@"><![CDATA[
+        #if $dup_to_ins.reference_source.reference_source_selector == 'history':
+            ln -f -s '$dup_to_ins.reference_source.ref_file' reference.fa &&
+        #else:
+            ln -f -s '$dup_to_ins.reference_source.ref_file.fields.path' reference.fa &&
+        #end if
+    ]]></token>
+
+    <xml name="reference">
+        <conditional name="reference_source">
+            <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
+                <option value="cached">Use a built-in genome</option>
+                <option value="history">Use a genome from history</option>
+            </param>
+            <when value="cached">
+                <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
+                    <options from_data_table="all_fasta">
+                        <filter type="sort_by" column="2"/>
+                        <validator type="no_options" message="No reference genomes are available"/>
+                    </options>
+                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+                </param>
+            </when>
+            <when value="history">
+                <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/>
+            </when>
+        </conditional>
+    </xml>
+    <!--
+        Help
+    -->
+
+    <token name="@WID@"><![CDATA[
+*Jasmine*, or Jointly Accurate Sv Merging with Intersample Network Edges is a tool used to merge structural variants (SVs) across samples. Each sample has a number of SV calls, consisting of position information (chromosome, start, end, length), type and strand information, and a number of other values. Jasmine represents the set of all SVs across samples as a network, and uses a modified minimum spanning forest algorithm to determine the best way of merging the variants such that each merged variants represents a set of analogous variants occurring in different samples.
+]]></token>
+    <token name="@REFERENCES@"><![CDATA[
+More information is available in the `github <https://github.com/mkirsche/Jasmine>`_.
+    ]]></token>
+</macros>