# HG changeset patch
# User boris
# Date 1374270363 14400
# Node ID 9453ba52f46b15dfca1fba85376a349797be99df
# Parent  dd39849c2ff1fe71750d42175e87de9ca81d08c8
tool now uses multiple selection for input fasta files

diff -r dd39849c2ff1 -r 9453ba52f46b phylorelatives.xml
--- a/phylorelatives.xml	Fri Jul 19 17:44:58 2013 -0400
+++ b/phylorelatives.xml	Fri Jul 19 17:46:03 2013 -0400
@@ -7,34 +7,31 @@
     <requirement type="package" version="3.0-8">ape</requirement>
   </requirements>
   <command interpreter="python">phylorelatives.py
-     #for $sequence in $sequences:
-         -i "${sequence.sequence}"
+     #for $sequence in ( $sequences ):
+         -i "${sequence}"
      #end for
      -m "${multifasta}"
      -b "$iterations"
      $pairwise
      $major_only
-     #if str($root.root_selector)=="upload_root":
+     #if str($root.root_selector)=="add_root":
       -r "${root.root_fa}"
      #end if
      --relatives-out "$siblings"
      --newick-out "$newick"
      --trees-out "$plot"
-
   </command>
   <inputs>
-    <repeat name="sequences" title="Input FASTA file" min="1" help="Files will be concatenated into a single FASTA multiple alignment file, thus equal length homologous sequences are required">
-      <param format="fasta" name="sequence" type="data" label="FASTA file" help="Minor allele sequences must be labeled &quot;_minor&quot; or &quot;_test&quot; e.g. &quot;>sample1_minor&quot;">
+      <param format="fasta" name="sequences" type="data" label="FASTA file" multiple="TRUE" help="Minor allele sequences must be labeled &quot;_minor&quot; or &quot;_test&quot; e.g. &quot;>sample1_minor&quot;">
       </param>
-    </repeat>
     <conditional name="root">
       <param name="root_selector" type="select" label=" Root sequence">
         <option value="unrooted" selected="True"></option>
-        <option value="upload_root"></option>
+        <option value="add_root"></option>
       </param>
       <when value="unrooted">
       </when>           
-      <when value="upload_root">
+      <when value="add_root">
         <param name="root_fa" format="fasta" type="data"  label="Root tree using" help="Must have the same length as input sequences"/>
       </when>
     </conditional>
@@ -51,7 +48,7 @@
   <tests>
     <test>
       <param name="iterations" value="0"/>
-      <param name="sequence" value="test.fa"/>
+      <param name="sequences" value="test.fa"/>
       <output name="siblings" file="test.fa-siblings.tab"/>
     </test>
   </tests>