From a0d6d113abc22312adea2b332192f6d6c12af0ac Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 21 Nov 2013 19:17:12 -0600
Subject: [PATCH] Add more sample tools for tool testing framework. Adding
 multi_select.xml, which demonstrates twill cannot deal with - at the
 beginning of select param values - this test works immediately with API
 interactor.

Also adding a multi_output.xml, this is a tool using variable number of outputs (force_refresh=True), both interactors pass this but it is a good test to verify that.

Also adding example to test multi-page tools (multi_page.xml) - both interactors pass this test. Though the API needed to be adjusted to allow its use (in a previous changeset).

Also adding example tool demonstrating extra_files output.

Finally, a tool simple_constructs.xml that just tests the basics, various parameter types, simple conditional, and simple repeat.
---
 test/functional/tools/composite_output.xml  | 24 +++++++++++
 test/functional/tools/multi_output.xml      | 22 ++++++++++
 test/functional/tools/multi_page.xml        | 29 +++++++++++++
 test/functional/tools/multi_select.xml      | 29 +++++++++++++
 test/functional/tools/samples_tool_conf.xml |  5 +++
 test/functional/tools/simple_constructs.xml | 47 +++++++++++++++++++++
 6 files changed, 156 insertions(+)
 create mode 100644 test/functional/tools/composite_output.xml
 create mode 100644 test/functional/tools/multi_output.xml
 create mode 100644 test/functional/tools/multi_page.xml
 create mode 100644 test/functional/tools/multi_select.xml
 create mode 100644 test/functional/tools/simple_constructs.xml

diff --git a/test/functional/tools/composite_output.xml b/test/functional/tools/composite_output.xml
new file mode 100644
index 00000000000..bdc21159a28
--- /dev/null
+++ b/test/functional/tools/composite_output.xml
@@ -0,0 +1,24 @@
+<tool id="composite_output" name="composite_output" version="1.0.0">
+  <command>mkdir $output.extra_files_path; cp $input.extra_files_path/* $output.extra_files_path</command>
+  <inputs>
+    <param name="input" type="data" format="velvet" label="Velvet Dataset" help="Prepared by velveth."/>
+  </inputs>
+  <outputs>
+    <data format="velvet" name="output" label="">
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="velveth_test1/output.html" ftype="velvet" >
+        <composite_data value='velveth_test1/Sequences' ftype="Sequences"/>
+        <composite_data value='velveth_test1/Roadmaps' ftype="Roadmaps"/>
+        <composite_data value='velveth_test1/Log'/>
+      </param>
+      <output name="output" file="velveth_test1/output.html">
+        <extra_files type="file" name="Sequences" value="velveth_test1/Sequences" />
+        <extra_files type="file" name="Roadmaps" value="velveth_test1/Roadmaps" />
+        <extra_files type="file" name="Log" value="velveth_test1/Log" />
+      </output>
+    </test>
+  </tests>
+</tool>
diff --git a/test/functional/tools/multi_output.xml b/test/functional/tools/multi_output.xml
new file mode 100644
index 00000000000..85bc86daa1c
--- /dev/null
+++ b/test/functional/tools/multi_output.xml
@@ -0,0 +1,22 @@
+<tool id="multi_output" name="Multi_Output" description="multi_output" force_history_refresh="True" version="0.1.0">
+  <command>
+    echo "Hello" > $report;
+    echo "World" > '${__new_file_path__}/primary_${report.id}_moo_visible_?'
+  </command>
+  <inputs>
+    <param name="input" type="integer" value="7" />
+  </inputs>
+  <outputs>
+    <data format="txt" name="report" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="7" />
+      <output name="report">
+        <assert_contents>
+          <has_line line="Hello" />
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+</tool>
diff --git a/test/functional/tools/multi_page.xml b/test/functional/tools/multi_page.xml
new file mode 100644
index 00000000000..a9dc042586a
--- /dev/null
+++ b/test/functional/tools/multi_page.xml
@@ -0,0 +1,29 @@
+<tool id="multi_page" name="Multi_Page" description="multi_page" version="0.1.0">
+  <configfiles>
+    <configfile name="config">${p1} ${p2}</configfile>
+  </configfiles>
+  <command>cat $config > $output</command>
+  <inputs>
+    <page>
+      <param name="p1" type="integer" value="1" />
+    </page>
+    <page>
+      <param name="p2" type="integer" value="2" />
+    </page>
+  </inputs>
+  <outputs>
+    <data format="txt" name="output" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="p1" value="3" />
+      <param name="p2" value="4" />
+
+      <output name="output">
+        <assert_contents>
+          <has_line line="3 4" />
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+</tool>
diff --git a/test/functional/tools/multi_select.xml b/test/functional/tools/multi_select.xml
new file mode 100644
index 00000000000..d1356157cae
--- /dev/null
+++ b/test/functional/tools/multi_select.xml
@@ -0,0 +1,29 @@
+<tool id="multi_select" name="multi_select" version="1.0.0">
+  <description>multi_select</description>
+  <configfiles>
+    <configfile name="config">${select_ex}</configfile>
+  </configfiles>
+  <command>cat $config > $output</command>
+  <inputs>
+    <param name="select_ex" type="select" display="checkboxes" multiple="true">
+      <option value="--ex1">Ex1</option>
+      <option value="ex2">Ex2</option>
+      <option value="--ex3">Ex3</option>
+      <option value="--ex4">Ex4</option>
+      <option value="ex5">Ex5</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="txt" name="output" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="select_ex" value="--ex1,ex2,--ex3" />
+      <output name="output">
+        <assert_contents>
+          <has_line line="--ex1,ex2,--ex3" />
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+</tool>
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index 676a5e877f9..cc05026efb8 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -1,7 +1,12 @@
 <?xml version="1.0"?>
 <toolbox>
   <tool file="upload.xml"/>
+  <tool file="simple_constructs.xml" />
   <tool file="composite.xml" />
   <tool file="disambiguate_cond.xml" />
   <tool file="multi_repeats.xml"/>
+  <tool file="multi_page.xml"/>
+  <tool file="multi_select.xml" />
+  <tool file="multi_output.xml" />
+  <tool file="composite_output.xml" />
 </toolbox>
\ No newline at end of file
diff --git a/test/functional/tools/simple_constructs.xml b/test/functional/tools/simple_constructs.xml
new file mode 100644
index 00000000000..b543af03a89
--- /dev/null
+++ b/test/functional/tools/simple_constructs.xml
@@ -0,0 +1,47 @@
+<tool id="simple_constructs" name="simple_constructs">
+    <command>
+        echo "$p1.p1val"  >> $out_file1;
+        echo "$booltest"  >> $out_file1;
+        echo "$inttest"   >> $out_file1; 
+        echo "$floattest" >> $out_file1; 
+        cat "$files[0].file"   >> $out_file1;
+    </command>
+    <inputs>
+        <conditional name="p1">
+            <param type="boolean" name="p1use" />
+            <when value="true">
+                <param name="p1val" value="p1used" type="text" />
+            </when>
+            <when value="false">
+                <param name="p1val" value="p1notused" type="text" />
+            </when>
+        </conditional>
+        <param name="booltest" truevalue="booltrue" falsevalue="boolfalse" checked="false" type="boolean" />
+        <param name="inttest" value="1" type="integer" />
+        <param name="floattest" value="1.0" type="float" />
+        <repeat name="files" title="Files">
+            <param name="file" type="data" format="txt" />
+        </repeat>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="p1use" value="true" />
+            <param name="booltest" value="true" />
+            <param name="inttest" value="12456" />
+            <param name="floattest" value="6.789" />
+            <param name="file" value="simple_line.txt" /> <!-- This is a line of text. -->
+            <output name="out_file1">
+                <assert_contents>
+                    <has_line line="p1used" />
+                    <has_line line="booltrue" />
+                    <has_line line="12456" />
+                    <has_line line="6.789" />
+                    <has_line line="This is a line of text." />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>