# HG changeset patch
# User artbio
# Date 1697020448 0
# Node ID 3041f611636f18216784936384b4325ad223dd55
# Parent  be61d0d0d622385740624e614ea9f155ab382bd1
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold commit 22c413141878d86ec10e80ef43ba0da792232cb0

diff -r be61d0d0d622 -r 3041f611636f blast_to_scaffold.xml
--- a/blast_to_scaffold.xml	Wed Mar 10 19:09:31 2021 +0000
+++ b/blast_to_scaffold.xml	Wed Oct 11 10:34:08 2023 +0000
@@ -3,14 +3,15 @@
 <requirements>
     <requirement type="package" version="3.7.6">python</requirement>
 </requirements>
-<command interpreter="python">
-        blast_to_scaffold.py --sequences "$sequences"
-                             --guideSequence "$guideSequence"
-                             --blast-tab "$blast_tab"
-                             --output "$output"
-                             --scaffold_prefix "$sequences.element_identifier"
-                             --scaffold_suffix "$guideSequence.element_identifier"
-</command>
+<command detect_errors="exit_code"><![CDATA[
+        python $__tool_directory__/blast_to_scaffold.py
+                                      --sequences "$sequences"
+                                      --guideSequence "$guideSequence"
+                                      --blast-tab "$blast_tab"
+                                      --output "$output"
+                                      --scaffold_prefix "$sequences.element_identifier"
+                                      --scaffold_suffix "$guideSequence.element_identifier"
+]]></command>
 <inputs>
 <param name="sequences" type="data" format="fasta" label="Select a fasta contigs file"/> 
 <param name="guideSequence" type="data" format="fasta" label="Select the fasta guide sequence for scaffolding"/> 
@@ -47,4 +48,8 @@
 This Galaxy tool was created by drosofff@gmail.com on 5/01/2016
 </help>
 
+<citations>
+    <citation type="doi">10.1186/s13742-015-0080-7</citation>
+</citations>
+
 </tool>