diff sed.xml @ 6:8928e6d1e7ba draft

Uploaded

--- a/sed.xml	Wed Jan 07 11:15:41 2015 -0500
+++ b/sed.xml	Thu Jan 08 09:07:31 2015 -0500
@@ -9,7 +9,7 @@
     <version_command>sed --version | head -n 1</version_command>
     <command>
 <![CDATA[
-        sed 
+        sed
             --sandbox
             -r
             #if $adv_opts.adv_opts_selector == 'advanced':
@@ -22,7 +22,7 @@
     </command>
     <inputs>
         <param format="txt" name="infile" type="data" label="File to process" />
-        <param name="url_paste" type="text" area="true" size="5x35" label="SED Program" help="">
+        <param name="code" type="text" area="true" size="5x35" label="SED Program" help="">
             <sanitizer>
                 <valid initial="string.printable">
                     <remove value="&apos;"/>
@@ -36,7 +36,7 @@
             </param>
             <when value="basic" />
             <when value="advanced">
-                <param name="silent" type="select"  label="operation mode" help="(Same as 'sed -n', leave at 'normal' unless you know what you're doing)" >
+                <param name="silent" type="select" label="Operation mode" help="Same as 'sed -n', leave at 'normal' unless you know what you're doing." >
                     <option value="">normal</option>
                     <option value="-n">silent</option>
                 </param>
@@ -45,24 +45,25 @@
     </inputs>
     <configfiles>
         <configfile name="sed_script">
-          $url_paste
+          $code
         </configfile>
     </configfiles>
     <outputs>
-        <data format="input" name="output" metadata_source="infile" />
+        <data name="output" format_source="infile" metadata_source="infile" />
     </outputs>
     <tests>
         <test>
-            <param name="infile" value="unix_sed_input1.txt" />
-            <param name="url_paste"  value="1d ; s/foo/bar/" />
+            <param name="infile" value="sed1.txt" />
+            <param name="code" value="1d ; s/foo/bar/" />
             <param name="silent" value="" />
-            <output name="output" file="unix_sed_output1.txt" />
+            <output name="output" file="sed_results1.txt" />
         </test>
         <test>
-            <param name="infile" value="unix_sed_input1.txt" />
-            <param name="url_paste"  value="/foo/ { s/foo/baz/g ; p }" />
-            <param name="silent" value="silent" />
-            <output name="output" file="unix_sed_output2.txt" />
+            <param name="infile" value="sed1.txt" />
+            <param name="code" value="/foo/ { s/foo/baz/g ; p }" />
+            <param name="adv_opts_selector" value="advanced" />
+            <param name="silent" value="-n" />
+            <output name="output" file="sed_results2.txt" />
         </test>
     </tests>
     <help>
@@ -95,8 +96,8 @@
 
 - **s/hsa//**  will remove the first instance of 'hsa' in every line.
 - **s/hsa//g**  will remove all instances (beacuse of the **g**) of 'hsa' in every line.
-- **s/A{4,}/--&amp;--/g**  will find sequences of 4 or more consecutive A's, and once found, will surround them with two dashes from each side. The **&amp;** marker is a place holder for 'whatever matched the regular expression'.
-- **s/hsa-mir-([^ ]+)/short name: \\1 full name: &amp;/**  will find strings such as 'hsa-mir-43a' (the regular expression is 'hsa-mir-' followed by non-space characters) and will replace it will string such as 'short name: 43a full name: hsa-mir-43a'.  The **\\1** marker is a place holder for 'whatever matched the first parenthesis' (similar to perl's **$1**) .
+- **s/A{4,}/--&--/g**  will find sequences of 4 or more consecutive A's, and once found, will surround them with two dashes from each side. The **&** marker is a place holder for 'whatever matched the regular expression'.
+- **s/hsa-mir-([^ ]+)/short name: \\1 full name: &/**  will find strings such as 'hsa-mir-43a' (the regular expression is 'hsa-mir-' followed by non-space characters) and will replace it will string such as 'short name: 43a full name: hsa-mir-43a'.  The **\\1** marker is a place holder for 'whatever matched the first parenthesis' (similar to perl's **$1**) .
 
 
 **sed's Regular Expression Syntax**