# HG changeset patch
# User galaxyp
# Date 1556304127 14400
# Node ID 23f34d9dd8e6504df12cb9cf536e98a6fb094c5e
# Parent  a873420ef8334c97f989a1cec47b754a48767431
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit e5ab6444aa2f104eedfa366bee05f65edef02d82

diff -r a873420ef833 -r 23f34d9dd8e6 gffcompare_to_bed.xml
--- a/gffcompare_to_bed.xml	Thu Jan 11 11:16:32 2018 -0500
+++ b/gffcompare_to_bed.xml	Fri Apr 26 14:42:07 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="gffcompare_to_bed" name="Convert gffCompare annotated GTF to BED" version="0.1.0">
+<tool id="gffcompare_to_bed" name="Convert gffCompare annotated GTF to BED" version="0.2.0">
     <description>for StringTie results</description>
     <command detect_errors="exit_code"><![CDATA[
         python '$__tool_directory__/gffcompare_to_bed.py'  
@@ -12,6 +12,7 @@
         <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="~">~ : Intron chain match or single-exon (gffcompare strict-match)</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>
@@ -47,6 +48,12 @@
     <help><![CDATA[
 Convert a GFFCompare annotated GTF file to BED format.
 
+A typical workflow:
+
+.. image:: GTF2Bed_workflow.png
+  :height: 308
+  :width: 750
+
 usage: gffcompare_to_bed.py [-h] [-C CLASS_CODE] [-v] [-d] input output
 
 positional arguments:
@@ -59,6 +66,9 @@
                         Restrict output to gffcompare class codes
   -d, --debug           Debug
 
+For class_code definitions see gffcompare documentation: 
+http://ccb.jhu.edu/software/stringtie/gffcompare.shtml#transfrag-class-codes
+
     ]]></help>
     <citations>
         <citation type="doi">10.1038/nbt.1621</citation>
diff -r a873420ef833 -r 23f34d9dd8e6 static/images/GTF2Bed_workflow.png
Binary file static/images/GTF2Bed_workflow.png has changed