Merge pull request #632 from ARTbio/blastx_to_scaffold

update blastx_to_scaffold tool

tools/blastx_to_scaffold/.shed.yml

@@ -13,8 +13,6 @@ categories:
   - Sequence Analysis
   - Assembly
 homepage_url: http://artbio.fr
-remote_repository_url: https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold
+remote_repository_url: https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold
 toolshed:
-  - https://lbcd41.snv.jussieu.fr/toolshed/
-  - testtoolshed
   - toolshed

tools/blastx_to_scaffold/blastx_to_scaffold.xml

@@ -1,13 +1,14 @@
-<tool id="blastx2scaffold" name="blastx_to_scaffold" version="1.1.0">
+<tool id="blastx2scaffold" name="blastx_to_scaffold" version="1.1.1">
 <description>Generate DNA scaffold from blastx alignment of Contigs</description>
 <requirements>
     <requirement type="package" version="3.7.6">python</requirement>
 </requirements>
-<command interpreter="python">
-        blastx_to_scaffold.py --sequences $sequences
+<command detect_errors="exit_code"><![CDATA[
+    python $__tool_directory__/blastx_to_scaffold.py
+                              --sequences $sequences
                               --blastx-tab $blastx_tab
                               --output $output
-</command>
+]]></command>
 <inputs>
 <param name="sequences" type="data" format="fasta" label="Select a fasta contigs file"/> 
 <param name="blastx_tab"  type="data" format="tabular" label="Select a blastx output from your history" help="must have 13 columns with column 13 containing the subject lenght, other columns are standard"/> 
@@ -32,12 +33,17 @@
 
 **What it Does**
 This tool starts from DNA contigs that aligned to a subject protein sequence through blastx.
-The contigs must be provided in fasta format. The blastx output must be tabular, the 12 standard column plus column 13 with the length of the blastx subject.
+The contigs must be provided in fasta format. The blastx output must be tabular, the 12 standard
+columns plus column 13 with the length of the blastx subject.
+
 The final scaffold is a DNA sequence.
+
 Sequences of the subject protein which were not aligned to the contigs are replaced by Ns in this scaffold.
 
-**Attribution**
-This Galaxy tool was created by [email protected] on 28/05/2015
 </help>
 
+<citations>
+    <citation type="doi">10.1186/s13742-015-0080-7</citation>
+</citations>
+
 </tool>