# HG changeset patch
# User abims-sbr
# Date 1516284144 18000
# Node ID e0bea88bb09fc4680175cdb21a82a8d421925531
# Parent  0d2da4c020dce4de0c0daadb9e215489d2babcc3
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 76e603ecd0118c8060d972b675a13db858956eb6

diff -r 0d2da4c020dc -r e0bea88bb09f BlastAlign.xml
--- a/BlastAlign.xml	Thu Jan 18 08:13:26 2018 -0500
+++ b/BlastAlign.xml	Thu Jan 18 09:02:24 2018 -0500
@@ -1,4 +1,4 @@
-<tool name="BlastAlign" id="blastalign" version="2.1">
+<tool name="BlastAlign" id="blastalign" version="2.0">
 
     <description>
         Align the nucleic acid sequences using BLASTN
@@ -55,10 +55,9 @@
     </inputs>
 
     <outputs>
-        <!-- 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" />
+        <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">
             <filter>fasta_out == True</filter>
         </data>
     </outputs>
@@ -105,6 +104,22 @@
             <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 0d2da4c020dc -r e0bea88bb09f scripts/S01_phylip2fasta.py
--- a/scripts/S01_phylip2fasta.py	Thu Jan 18 08:13:26 2018 -0500
+++ b/scripts/S01_phylip2fasta.py	Thu Jan 18 09:02:24 2018 -0500
@@ -13,14 +13,12 @@
 """
 
 ## 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
@@ -52,7 +50,10 @@
 ###################
 
 F1.readline() ## jump the first line
+
 fichier_txt, c = format(F1)   ### DEF1 ###
+
 F2.write(fichier_txt)
+
 F1.close()
 F2.close()