--- a/grep.xml	Sun Oct 06 08:22:36 2013 -0400
+++ b/grep.xml	Wed Jan 07 11:10:52 2015 -0500
@@ -1,21 +1,42 @@
-<tool id="tp_grep_tool" name="Search in textfiles" version="0.1.1">
+<tool id="tp_grep_tool" name="Search in textfiles" version="@BASE_VERSION@.0">
     <description>(grep)</description>
-    <requirements>
-        <requirement type="package" version="8.21">gnu_coreutils</requirement>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
         <requirement type="package" version="2.14">gnu_grep</requirement>
         <requirement type="set_environment">TP_SCRIPT_PATH</requirement>
-    </requirements>
+    </expand>
+    <version_command>grep --version | head -n 1</version_command>
     <command>
+<![CDATA[
         #if str($color) == "COLOR":
-            GREP_COLOR='1;34' grep --color=always -P "$@" -- "${url_paste}" '${input}' | \$TP_SCRIPT_PATH/ansi2html.sh > "${output}"
+            GREP_COLOR='1;34'
+            grep
+                --color=always
+                -P
+                -A $lines_after
+                -B $lines_before
+                $invert
+                $case_sensitive
+                -- "${url_paste}"
+                '${infile}' | \$TP_SCRIPT_PATH/ansi2html.sh > "${output}"
         #else:
-            grep -P "$@" -- "${url_paste}" '${input}' | grep -v "^--$" > "${output}"
+            grep
+                -P
+                -A $lines_after
+                -B $lines_before
+                $invert
+                $case_sensitive
+                 -- "${url_paste}"
+                '${infile}' | grep -v "^--$" > "${output}"
         #end if
 
-        ##grep_wrapper.sh '$input' '$output' '$url_paste' $color -A $lines_after -B $lines_before $invert $case_sensitive
+        ##grep_wrapper.sh '$infile' '$output' '$url_paste' $color -A $lines_after -B $lines_before $invert $case_sensitive
+]]>
     </command>
     <inputs>
-        <param format="txt" name="input" type="data" label="Select lines from" />
+        <param name="infile" format="txt" type="data" label="Select lines from" />
 
         <param name="invert" type="select" label="that">
             <option value="">Match</option>
@@ -30,55 +51,54 @@
             </sanitizer>
         </param>
 
-        <param name="case_sensitive" type="select"  label="Match type">
+        <param name="case_sensitive" type="select" label="Match type" help="(-i)">
             <option value="-i">case insensitive</option>
             <option value="">case sensitive</option>
         </param>
-
-        <param name="lines_before" type="integer"  label="Show lines preceding the matched line (-B)" help="leave it at zero unless you know what you're doing" value="0" />
-        <param name="lines_after" type="integer"  label="Show lines trailing the matched line (-A)" help="leave it at zero unless you know what you're doing" value="0" />
-
+        <param name="lines_before" type="integer" value="0"
+            label="Show lines preceding the matched line" help="leave it at zero unless you know what you're doing. (-B)" />
+        <param name="lines_after" type="integer" value="0"
+            label="Show lines trailing the matched line" help="leave it at zero unless you know what you're doing. (-A)" />
         <param name="color" type="select"  label="Output">
             <option value="NOCOLOR">text file (for further processing)</option>
             <option value="COLOR">Highlighted HTML (for easier viewing)</option>
         </param>
 
-  </inputs>
-  <outputs>
-      <data format="input" name="output" metadata_source="input">
-        <change_format>
-            <when input="color" value="COLOR" format="html"
-            />
-        </change_format>
-      </data>
-  </outputs>
-  <tests>
-      <test>
-          <!-- grep a FASTA file for sequences with specific motif -->
-          <param name="input" value="unix_grep_input1.txt" />
-          <output name="output" file="unix_grep_output1.txt" />
-          <param name="case_sensitive" value="case sensitive" />
-          <param name="invert" value="" />
-          <param name="url_paste" value="AA.{2}GT" />
-          <param name="lines_before" value="1" />
-          <param name="lines_after" value="0" />
-          <param name="color" value="NOCOLOR" />
-      </test>
-      <test>
-          <!-- grep a FASTA file for sequences with specific motif -
+    </inputs>
+    <outputs>
+        <data format="input" name="output" metadata_source="infile">
+            <change_format>
+                <when input="color" value="COLOR" format="html"/>
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <!-- grep a FASTA file for sequences with specific motif -->
+            <param name="infile" value="unix_grep_input1.txt" />
+            <param name="case_sensitive" value="case sensitive" />
+            <param name="invert" value="" />
+            <param name="url_paste" value="AA.{2}GT" />
+            <param name="lines_before" value="1" />
+            <param name="lines_after" value="0" />
+            <param name="color" value="NOCOLOR" />
+            <output name="output" file="unix_grep_output1.txt" />
+        </test>
+        <test>
+            <!-- grep a FASTA file for sequences with specific motif -
              show highlighed output -->
-          <param name="input" value="unix_grep_input1.txt" />
-          <output name="output" file="unix_grep_output2.html" />
-          <param name="case_sensitive" value="case sensitive" />
-          <param name="invert" value="" />
-          <param name="url_paste" value="AA.{2}GT" />
-          <param name="lines_before" value="0" />
-          <param name="lines_after" value="0" />
-          <param name="color" value="COLOR" />
-      </test>
-  </tests>
-<help>
-
+            <param name="infile" value="unix_grep_input1.txt" />
+            <param name="case_sensitive" value="case sensitive" />
+            <param name="invert" value="" />
+            <param name="url_paste" value="AA.{2}GT" />
+            <param name="lines_before" value="0" />
+            <param name="lines_after" value="0" />
+            <param name="color" value="COLOR" />
+            <output name="output" file="unix_grep_output2.html" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
 **What it does**
 
 This tool runs the unix **grep** command on the selected data file.
@@ -139,6 +159,7 @@
 - **$** matches the end of a line or string.
 - **\|** Separates alternate possibilities. 
 
-
-</help>
+@REFERENCES@
+]]>
+    </help>
 </tool>