# HG changeset patch
# User John Chilton <jmchilton@gmail.com>
# Date 1391911775 21600
# Node ID 5f452975cfb40f50307a4ad45e7f52d16296e44e

Initial commit.

diff -r 000000000000 -r 5f452975cfb4 disambiguate_cond.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/disambiguate_cond.xml	Sat Feb 08 20:09:35 2014 -0600
@@ -0,0 +1,94 @@
+<tool id="disambiguate_cond" name="disambiguate_cond">
+    <command>
+        echo "$p1.p1v $p2.p2v $p3.p3v" > $out_file1; cat "$files.p4.file" >> $out_file1;
+    </command>
+    <inputs>
+        <conditional name="p1">
+            <param type="boolean" name="use" />
+            <when value="true">
+                <param name="p1v" value="4" type="integer" />
+            </when>
+            <when value="false">
+                <param name="p1v" value="7" type="integer" />
+            </when>
+        </conditional>
+        <conditional name="p2">
+            <param type="boolean" name="use" />
+            <when value="true">
+                <param name="p2v" value="4" type="integer" />
+            </when>
+            <when value="false">
+                <param name="p2v" value="7" type="integer" />
+            </when>            
+        </conditional>
+        <conditional name="p3">
+            <param type="boolean" name="use" />
+            <when value="true">
+                <param name="p3v" value="4" type="integer" />
+            </when>
+            <when value="false">
+                <param name="p3v" value="7" type="integer" />
+            </when>            
+        </conditional>
+        <conditional name="files">
+            <param name="attach_files" type="boolean" checked="true" />
+            <when value="true">
+                <conditional name="p4">
+                    <param type="boolean" name="use" />
+                    <when value="true">
+                        <param type="data" name="file" />
+                    </when>
+                </conditional>
+            </when>
+        </conditional>               
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+    <tests interactor="api">
+        <!-- Can use nested conditional blocks as shown below to disambiguate
+             various nested parameters. -->
+        <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>
+        <!-- Can also use a more concise, flat verison of this, but it the
+             above version is more clear and should be considered preferable.
+        -->
+        <test>
+            <param name="p1|use" value="True"/>
+            <param name="p2|use" value="False"/>
+            <param name="p3|use" value="True"/>
+            <param name="p4|use" value="True" />
+            <!-- Only need to specify enough of a suffix to disambiguate,
+                 but don't do this - it is too clever. -->
+            <param name="p4|file" value="simple_line.txt" />
+            <output name="out_file1">
+                <assert_contents>
+                    <has_line line="4 7 4" />
+                    <has_line line="This is a line of text." />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff -r 000000000000 -r 5f452975cfb4 disambiguate_repeats.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/disambiguate_repeats.xml	Sat Feb 08 20:09:35 2014 -0600
@@ -0,0 +1,63 @@
+<tool id="disambiguate_repeats" name="disambiguate_repeats">
+    <command>
+        cat #for $q in $queries# ${q.input} #end for# #for $q in $more_queries# ${q.input} #end for# > $out_file1
+    </command>
+    <inputs>
+        <repeat name="queries" title="Dataset">
+            <param name="input" type="data" label="Select" />
+        </repeat>
+        <repeat name="more_queries" title="Dataset">
+            <param name="input" type="data" label="Select" />
+        </repeat>        
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+    <tests>
+        <!-- Can disambiguate repeats and specify multiple blocks using,
+             nested structure. -->
+        <test interactor="api">
+            <repeat name="queries">
+                <param name="input" value="simple_line.txt"/>
+            </repeat>
+            <repeat name="more_queries">
+                <param name="input" value="simple_line_alternative.txt"/>
+            </repeat>
+            <output name="out_file1">
+                <assert_contents>
+                    <has_line line="This is a line of text." />
+                    <has_line line="This is a different line of text." />
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Multiple such blocks can be specified but only with newer API
+             driven tests. -->
+        <test interactor="api">
+            <repeat name="queries">
+                <param name="input" value="simple_line.txt"/>
+            </repeat>
+            <repeat name="queries">
+                <param name="input" value="simple_line_alternative.txt"/>
+            </repeat>
+            <repeat name="more_queries">
+                <param name="input" value="simple_line.txt"/>
+            </repeat>
+            <repeat name="more_queries">
+                <param name="input" value="simple_line_alternative.txt"/>
+            </repeat>
+            <output name="out_file1" file="simple_lines_interleaved.txt"/>
+        </test>
+        <!-- Can also use prefixes to disambiguate inputs or force order, but
+             the above nested structure is preferable. -->
+        <test interactor="api">
+            <param name="queries_1|input" value="simple_line_alternative.txt"/>
+            <param name="queries_0|input" value="simple_line.txt"/>
+
+            <param name="more_queries_1|input" value="simple_line_alternative.txt" />
+            <param name="more_queries_0|input" value="simple_line.txt"/>
+
+            <output name="out_file1" file="simple_lines_interleaved.txt"/>
+        </test>
+
+    </tests>
+</tool>
diff -r 000000000000 -r 5f452975cfb4 test-data/simple_line.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/simple_line.txt	Sat Feb 08 20:09:35 2014 -0600
@@ -0,0 +1,1 @@
+This is a line of text.
diff -r 000000000000 -r 5f452975cfb4 test-data/simple_line_alternative.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/simple_line_alternative.txt	Sat Feb 08 20:09:35 2014 -0600
@@ -0,0 +1,1 @@
+This is a different line of text.
\ No newline at end of file
diff -r 000000000000 -r 5f452975cfb4 test-data/simple_line_x2.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/simple_line_x2.txt	Sat Feb 08 20:09:35 2014 -0600
@@ -0,0 +1,2 @@
+This is a line of text.
+This is a line of text.
diff -r 000000000000 -r 5f452975cfb4 test-data/simple_line_x3.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/simple_line_x3.txt	Sat Feb 08 20:09:35 2014 -0600
@@ -0,0 +1,3 @@
+This is a line of text.
+This is a line of text.
+This is a line of text.
diff -r 000000000000 -r 5f452975cfb4 test-data/simple_line_x5.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/simple_line_x5.txt	Sat Feb 08 20:09:35 2014 -0600
@@ -0,0 +1,5 @@
+This is a line of text.
+This is a line of text.
+This is a line of text.
+This is a line of text.
+This is a line of text.
diff -r 000000000000 -r 5f452975cfb4 test-data/simple_lines_interleaved.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/simple_lines_interleaved.txt	Sat Feb 08 20:09:35 2014 -0600
@@ -0,0 +1,4 @@
+This is a line of text.
+This is a different line of text.
+This is a line of text.
+This is a different line of text.
\ No newline at end of file