From c6d3679b9236faf50223abcf915db9cc58b9971b Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 21 Nov 2013 21:17:04 -0600
Subject: [PATCH] Clean up tool framework test tools. Add example of nested
 conditional disambiugation.

---
 test/functional/tools/composite.xml         |  3 +--
 test/functional/tools/disambiguate_cond.xml | 28 ++++++++++++++++++---
 test/functional/tools/multi_repeats.xml     |  3 +--
 3 files changed, 27 insertions(+), 7 deletions(-)

diff --git a/test/functional/tools/composite.xml b/test/functional/tools/composite.xml
index 902f28f3e58..497aa0cbbf9 100644
--- a/test/functional/tools/composite.xml
+++ b/test/functional/tools/composite.xml
@@ -1,5 +1,4 @@
-<tool id="velvet_inspired" name="velvet_inspired" version="1.0.0">
-  <description>Velvet sequence assembler for very short reads</description>
+<tool id="composite" version="1.0.0">
   <command>cat '$input.extra_files_path/Sequences' > $output</command>
   <inputs>
     <param name="input" type="data" format="velvet" label="Velvet Dataset" help="Prepared by velveth."/>
diff --git a/test/functional/tools/disambiguate_cond.xml b/test/functional/tools/disambiguate_cond.xml
index a757a5e2206..f55b98edec1 100644
--- a/test/functional/tools/disambiguate_cond.xml
+++ b/test/functional/tools/disambiguate_cond.xml
@@ -1,6 +1,4 @@
-<tool id="handle_cond" name="handle_cond">
-    <description>tail-to-head</description>
-    <!--  -->
+<tool id="disambiguate_cond" name="disambiguate_cond">
     <command>
         echo "$p1.p1v $p2.p2v $p3.p3v" > $out_file1; cat "$files.p4.file" >> $out_file1;
     </command>
@@ -61,5 +59,29 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <conditional name="p1">
+                <param name="use" value="False"/>
+            </conditional>
+            <conditional name="p2">
+                <param name="use" value="True"/>
+            </conditional>
+            <conditional name="p3">
+                <param name="use" value="False"/>
+            </conditional>            
+            <conditional name="files">
+                <param name="attach_files" value="True" />
+                <conditional name="p4">
+                    <param name="use" value="True"/>
+                    <param name="file" value="simple_line_alternative.txt" />
+                </conditional>
+            </conditional>
+            <output name="out_file1">
+                <assert_contents>
+                    <has_line line="7 4 7" />
+                    <has_line line="This is a different line of text." />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
 </tool>
diff --git a/test/functional/tools/multi_repeats.xml b/test/functional/tools/multi_repeats.xml
index 7447c544a32..745cb863115 100644
--- a/test/functional/tools/multi_repeats.xml
+++ b/test/functional/tools/multi_repeats.xml
@@ -1,5 +1,4 @@
-<tool id="multirepeat" name="multirepeat">
-    <description>tail-to-head</description>
+<tool id="multi_repeats" name="multi_repeats">
     <command>
         cat $input1 #for $q in $queries# ${q.input2} #end for# #for $q in $more_queries# ${q.more_queries_input} #end for# > $out_file1
     </command>