--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deconstruct.xml	Thu Apr 09 04:36:41 2020 -0400
@@ -0,0 +1,82 @@
+<tool id="vg_deconstruct" name="vg deconstruct" version="@TOOL_VERSION@">
+    <description>construct a dynamic succinct variation graph</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+ln -s '$infile' ./infile.${infile.ext} &&
+
+vg deconstruct
+#if $path:
+    --path '${','.join([$p for $p in $path])}'
+#end if
+#if $path_prefix
+    --path-prefix '${','.join([$p for $p in $path_prefix])}'
+#end if
+#if $alt_prefix
+    --alt-prefix '${','.join([$p for $p in $alt_prefix])}'
+#end if
+#if $snarls:
+    --snarls '$snarls'
+#end if
+$path_traversals  ## -e
+--threads=\${GALAXY_SLOTS:-1}
+./infile.${infile.ext}
+
+> '$output'
+
+    ]]></command>
+    <inputs>
+        <param name="infile" type="data" format="xg,odgi" label="Graph files" />
+        <param argument="--path" type="text" value="" label="A reference path to deconstruct against"
+            help="comma-separated list accepted">
+            <sanitizer>
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param argument="--path-prefix" type="text" value="" label="All paths beginning with this value used as reference"
+            help="comma-separated list accepted">
+            <sanitizer>
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param argument="--alt-prefix" type="text" value="" label="Non-reference paths beginning with with this value get lumped together to same sample in VCF"
+            help="comma-separated list accepted">
+            <sanitizer>
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <param argument="--snarls" type="data" format="xg,odgi" label="Snarls files" optional="true"
+            help="from `vg snarls` to avoid recomputing" />
+
+        <param argument="--path-traversals" type="boolean" truevalue="--path-traversals" falsevalue="" checked="false"
+            label="Only consider traversals that correspond to paths in the grpah" />
+    </inputs>
+    <outputs>
+        <data name="output" format="vcf" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="hla.xg" />
+            <param name="path" value="gi|568815592:29791752-29792749" />
+            <param name="path_traversals" value="true" />
+            <output name="output" file="hla_variants.vcf" />
+        </test>
+    </tests>
+    <help><![CDATA[
+variation graph (vg) deconstruct module
+-----------------------------------
+
+Creates VCF records for Snarls present in a graph (relative to a chosen reference path).
+
+    ]]></help>
+    <expand macro="citations">
+    </expand>
+</tool>