--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gffcompare_to_bed.xml	Thu Jan 11 11:16:51 2018 -0500
@@ -0,0 +1,66 @@
+<tool id="gffcompare_to_bed" name="Convert gffCompare annotated GTF to BED" version="0.1.0">
+    <description>for StringTie results</description>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/gffcompare_to_bed.py'  
+        #if $class_codes:
+            --class_code='$class_codes'
+        #end if
+        $input $output
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="gtf" label="GTF annotated by gffCompare"/>
+        <param name="class_codes" type="select" display="checkboxes" multiple="true" optional="true" 
+            label="filter gffCompare class_codes to convert" help="No selection implies no filtering">
+            <option value="=">= : Complete match of intron chain</option>
+            <option value="c">c : Contained</option>
+            <option value="j">j : Potentially novel isoform (fragment): at least one splice junction is shared with a reference transcript</option>
+            <option value="e">e : Single exon transfrag overlapping a reference exon and at least 10 bp of a reference intron, indicating a possible pre-mRNA fragment.</option>
+            <option value="i">i : A transfrag falling entirely within a reference intron</option>
+            <option value="o">o : Generic exonic overlap with a reference transcript</option>
+            <option value="p">p : Possible polymerase run-on fragment (within 2Kbases of a reference transcript)</option>
+            <option value="r">r : Repeat. Currently determined by looking at the soft-masked reference sequence and applied to transcripts where at least 50% of the bases are lower case</option>
+            <option value="u">u : Unknown, intergenic transcript</option>
+            <option value="x">x : Exonic overlap with reference on the opposite strand</option>
+            <option value="s">s : An intron of the transfrag overlaps a reference intron on the opposite strand (likely due to read mapping errors)</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="bed" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="gffcompare_annotated.gtf" ftype="gtf"/>
+            <output name="output" file="gffcompare_output.bed"/>
+        </test>
+        <test>
+            <param name="input" value="gffcompare_annotated.gtf" ftype="gtf"/>
+            <param name="class_codes" value="j"/>
+            <output name="output" file="gffcompare_output_j.bed"/>
+        </test>
+        <test>
+            <param name="input" value="gffcompare_annotated.gtf" ftype="gtf"/>
+            <param name="class_codes" value="j,e,i,p,u,x"/>
+            <output name="output" file="gffcompare_output_jeipux.bed"/>
+        </test>
+
+    </tests>
+    <help><![CDATA[
+Convert a GFFCompare annotated GTF file to BED format.
+
+usage: gffcompare_to_bed.py [-h] [-C CLASS_CODE] [-v] [-d] input output
+
+positional arguments:
+  input                 GFFCompare annotated GTF file, (-) for stdin
+  output                BED file, (-) for stdout
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -C CLASS_CODE, --class_code CLASS_CODE
+                        Restrict output to gffcompare class codes
+  -d, --debug           Debug
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1038/nbt.1621</citation>
+    </citations>
+</tool>