# HG changeset patch
# User lecorguille
# Date 1537775961 14400
# Node ID 5cae58aa118152cbaa15fba5baae4c429ee3c51d
# Parent  ff1a3a7903636f253a0377d6df74078f638a2d2c
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1

diff -r ff1a3a790363 -r 5cae58aa1181 ConcatPhyl.xml
--- a/ConcatPhyl.xml	Tue Jul 03 10:55:20 2018 -0400
+++ b/ConcatPhyl.xml	Mon Sep 24 03:59:21 2018 -0400
@@ -160,12 +160,12 @@
 
 		<param name="out" type="select" label="What format of file do you want for your output (concatenation of the sequences) ? ">
 			<option value="nothing">No output</option>
-			<option value="fasta">Fasta format</option>
+			<option value="fasta" selected="true">Fasta format</option>
 			<option value="phylip">Phylip format</option>
 			<option value="nexus">Nexus format</option>
 		</param>
 		
-		<param name="raxml1" type="boolean" label="Do you want the output of RAxML : best tree ? " />
+		<param name="raxml1" type="boolean" checked="True" label="Do you want the output of RAxML : best tree ? " />
 		<param name="raxml3" type="boolean" label="Do you want the output of RAxML : bi-partition ? " />
 		<param name="raxml4" type="boolean" label="Do you want the output of RAxML : bootstrap ? " help="Only if the option 'rapid bootsptrap' is chosen. When you don't want to choose your options, this output is accessible"/>
 
@@ -285,18 +285,6 @@
 
 <![CDATA[
 
-.. class:: infomark
-
-**Authors**
-The run RAxML was written by Alexandros Stamatakis.
-The script was written by Eric Fontanillas.
-
-.. class:: infomark
-
-**Galaxy integration** by Julie Baffard and ABiMS team.
-
---------
-
 **Description**
 
 This tool takes files containing fasta sequences (from the CDS_Search in the AdaptSearch suite) and run RAxML to build a phylogeny.
@@ -413,6 +401,8 @@
 
 	</help>
 
-	<expand macro="citations" />
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btu033</citation>
+    </citations>
 
 </tool>
diff -r ff1a3a790363 -r 5cae58aa1181 macros.xml
--- a/macros.xml	Tue Jul 03 10:55:20 2018 -0400
+++ b/macros.xml	Mon Sep 24 03:59:21 2018 -0400
@@ -7,13 +7,14 @@
     <token name="@HELP_AUTHORS@">
 .. class:: infomark
 
-**Authors**  Eric Fontanillas creates the scripts of this pipeline.
+**Authors**  Eric Fontanillas created the version 1 of this pipeline. Victor Mataigne developped version 2.
 
 .. class:: infomark
 
-**Galaxy integration** ABiMS TEAM
+**Galaxy integration** Julie Baffard and ABiMS TEAM, Roscoff Marine Station
 
  | Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool.
+ | Credits : Gildas le Corguillé, Misharl Monsoor
 
 ---------------------------------------------------