# HG changeset patch
# User abims-sbr
# Date 1516281206 18000
# Node ID 0d2da4c020dce4de0c0daadb9e215489d2babcc3
# Parent  9eb5bb56bf41056540367d29f4aec6ddfe518b27
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit df6ba874c5e5f0cde12c9253b5c192e4a35f2280

diff -r 9eb5bb56bf41 -r 0d2da4c020dc BlastAlign.xml
--- a/BlastAlign.xml	Wed Jan 17 11:32:39 2018 -0500
+++ b/BlastAlign.xml	Thu Jan 18 08:13:26 2018 -0500
@@ -1,4 +1,4 @@
-<tool name="BlastAlign" id="blastalign" version="2.0">
+<tool name="BlastAlign" id="blastalign" version="2.1">
 
     <description>
         Align the nucleic acid sequences using BLASTN
@@ -55,9 +55,10 @@
     </inputs>
 
     <outputs>
-        <data format="phylip" name="phy" from_work_dir="out.phy" label="Alignment of ${input.name} in phylip" hidden="True"/>
-        <data format="nexus" name="nxs" from_work_dir="out.nxs" label="Alignment of ${input.name} in nexus" hidden="True"/>
-        <data format="fasta" name="fasta" from_work_dir="out.fasta" label="Alignment of ${input.name} in fasta" hidden="True">
+        <!-- visible="true" ? -->
+        <data format="phylip" name="phy" from_work_dir="out.phy" label="Alignment of ${input.name} in phylip" />
+        <data format="nexus" name="nxs" from_work_dir="out.nxs" label="Alignment of ${input.name} in nexus" />
+        <data format="fasta" name="fasta" from_work_dir="out.fasta" label="Alignment of ${input.name} in fasta" />
             <filter>fasta_out == True</filter>
         </data>
     </outputs>
@@ -104,22 +105,6 @@
             <output name="phy" value="outputs/locus3_sp2.phy" />
             <output name="nxs" value="outputs/locus3_sp2.nxs" />
         </test>
-        <test>
-            <param name="input" ftype="fasta" value="inputs/locus8_sp2.fasta" />
-            <section name="advanced_option">
-                <param name="m" value="95" />
-                <param name="r" value="" />
-                <param name="x" value="" />
-                <param name="n" value="False" />
-                <param name="s" value="0" />
-            </section>
-            <param name="fasta_out" value="True" />
-            <output name="phy" value="outputs/locus8_sp2.phy" />
-            <output name="nxs" value="outputs/locus8_sp2.nxs" />
-            <output name="fasta" value="outputs/locus8_sp2.fasta" />
-        </test>
-
-        <!--locus10_sp2.fasta    locus1_sp3.fasta  locus2_sp2.fasta  locus3_sp2.fasta  locus4_sp2.fasta  locus5_sp2.fasta  locus6_sp2.fasta  locus7_sp2.fasta  locus8_sp2.fasta  locus9_sp2.fasta-->
     </tests>
 
     <help>
diff -r 9eb5bb56bf41 -r 0d2da4c020dc scripts/S01_phylip2fasta.py
--- a/scripts/S01_phylip2fasta.py	Wed Jan 17 11:32:39 2018 -0500
+++ b/scripts/S01_phylip2fasta.py	Thu Jan 18 08:13:26 2018 -0500
@@ -13,12 +13,14 @@
 """
 
 ## INPUT
+"""
 if os.path.isfile(sys.argv[1]) :
     f1 = sys.argv[1]
 else:
     print "No existing phylip file ; exiting ..."
     exit()
-
+"""
+f1 = sys.argv[1]
 F1 = open("%s" %f1, 'r')
 
 ## OUTPUT
@@ -50,10 +52,7 @@
 ###################
 
 F1.readline() ## jump the first line
-
 fichier_txt, c = format(F1)   ### DEF1 ###
-
 F2.write(fichier_txt)
-
 F1.close()
 F2.close()