# HG changeset patch
# User iuc
# Date 1531245010 14400
# Node ID 91f27e8a25358ec78840cab12c02e74d81ad769f
# Parent  ca1320644fad1c7f8a67f22ee219704bfc9a6927
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 513a54a013c5762aa6099fe044b2d3acf4a76881

diff -r ca1320644fad -r 91f27e8a2535 coords2clnt.xml
--- a/coords2clnt.xml	Wed Apr 18 04:05:16 2018 -0400
+++ b/coords2clnt.xml	Tue Jul 10 13:50:10 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="bctools_extract_crosslinked_nucleotides" name="Get crosslinked nucleotides" version="@VERSION@">
+<tool id="bctools_extract_crosslinked_nucleotides" name="Get crosslinked nucleotides" version="@VERSION+galaxy1">
     <description>from full alignments</description>
     <macros>
         <import>macros.xml</import>
@@ -6,11 +6,15 @@
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         coords2clnt.py
+        $threeprime 
         '$alignment_coordinates'
         > '$crosslinking_coordinates'
     ]]></command>
     <inputs>
         <param name="alignment_coordinates" type="data" format="bed" label="Alignments in BED format"/>
+        <param argument="--threeprime" type="boolean" truevalue="--threeprime" falsevalue="" checked="false"
+            label="Set position one nt downstream of 3'-end as crosslinked nucleotide"
+            help="Set position one nt downstream of 3'-end as crosslinked nucleotide. By default the crosslink site will be assumed to be one nt upstream of the 5'-end of the read."/>
     </inputs>
     <outputs>
         <data name="crosslinking_coordinates" format="bed"/>