--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Dec 17 17:26:32 2019 -0500
@@ -0,0 +1,88 @@
+<macros>
+    <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy</token>
+    <token name="@TOOL_VERSION@">2.1.3.1</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">lofreq</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/nar/gks918</citation>
+            <yield />
+        </citations>
+    </xml>
+    <token name="@PREPARE_REF@"><![CDATA[
+        #if str($reference_source.ref_selector) == 'history':
+            #set $reference_fasta_fn = 'reference.fa'
+            ln -s '$reference_source.ref' $reference_fasta_fn &&
+            lofreq faidx $reference_fasta_fn 2>&1 || echo "Error running samtools faidx for indexing fasta reference for lofreq" >&2 &&
+        #else
+            #set $reference_fasta_fn = str($reference_source.ref.fields.path)
+        #end if
+    ]]></token>
+    <xml name="reference_interface">
+        <conditional name="reference_source">
+            <param name="ref_selector" type="select"
+            label="Choose the source for the reference genome">
+                <option value="cached">Locally cached</option>
+                <option value="history">History</option>
+            </param>
+            <when value="cached">
+                <param argument="--ref" type="select"
+                label="Reference genome">
+                    <options from_data_table="fasta_indexes">
+                        <filter type="data_meta" column="dbkey" key="dbkey" ref="reads" />
+                        <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param argument="--ref" type="data" format="fasta" label="Reference" help="Reference sequence" />
+            </when>
+        </conditional>
+    </xml>
+    <xml name="handle_existing_alnqual">
+        <conditional name="alnqual_choice">
+            <param name="alnquals_to_use" type="select"
+            label="Use the following alignment quality scores">
+                <option value="">Base and indel alignment qualities (BAQ and IDAQ)</option>
+                <option value="-A">Only base alignment qualities (BAQ)</option>
+                <option value="-B">Only indel alignment qualities (IDAQ)</option>
+            </param>
+            <when value="-B">
+                <param name="extended_baq" type="hidden" value="" />
+            </when>
+            <when value="">
+                <param argument="-e" name="extended_baq" type="boolean" checked="true" truevalue="" falsevalue="-e"
+                label="If BAQ needs to be computed, calculate extended BAQ?" />
+            </when>
+            <when value="-A">
+                <param argument="-e" name="extended_baq" type="boolean" checked="true" truevalue="" falsevalue="-e"
+                label="If BAQ needs to be computed, calculate extended BAQ?" />
+            </when>
+        </conditional>
+    </xml>
+    <xml name="handle_alnqual" token_mode="Use">
+        <conditional name="alnqual_choice">
+            <param name="alnquals_to_use" type="select"
+            label="@MODE@ the following alignment quality scores">
+                <option value="">Base and indel alignment qualities (BAQ and IDAQ)</option>
+                <option value="-A">Only base alignment qualities (BAQ)</option>
+                <option value="-B">Only indel alignment qualities (IDAQ)</option>
+            </param>
+            <when value="-B">
+                <param name="extended_baq" type="hidden" value="" />
+            </when>
+            <when value="">
+                <param argument="-e" name="extended_baq" type="boolean" checked="true" truevalue="" falsevalue="-e"
+                label="Use extended BAQ?" />
+            </when>
+            <when value="-A">
+                <param argument="-e" name="extended_baq" type="boolean" checked="true" truevalue="" falsevalue="-e"
+                label="Use extended BAQ?" />
+            </when>
+        </conditional>
+    </xml>
+</macros>