diff sed.xml @ 0:5314e5d6f040 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sed.xml	Thu Jan 29 07:53:17 2015 -0500
@@ -0,0 +1,133 @@
+<tool id="tp_sed_tool" name="Text transformation" version="@BASE_VERSION@.0">
+    <description>with sed</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="4.2.2-sandbox">gnu_sed</requirement>
+    </expand>
+    <version_command>sed --version | head -n 1</version_command>
+    <command>
+<![CDATA[
+        sed
+            --sandbox
+            -r
+            #if $adv_opts.adv_opts_selector == 'advanced':
+                $adv_opts.silent
+            #end if
+            -f '$sed_script'
+            '$infile'
+        > '$output'
+]]>
+    </command>
+    <inputs>
+        <param format="txt" name="infile" type="data" label="File to process" />
+        <param name="code" type="text" area="true" size="5x35" label="SED Program" help="">
+            <sanitizer>
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+        <conditional name="adv_opts">
+            <param name="adv_opts_selector" type="select" label="Advanced Options">
+              <option value="basic" selected="True">Hide Advanced Options</option>
+              <option value="advanced">Show Advanced Options</option>
+            </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." >
+                    <option value="">normal</option>
+                    <option value="-n">silent</option>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+    <configfiles>
+        <configfile name="sed_script">
+          $code
+        </configfile>
+    </configfiles>
+    <outputs>
+        <data name="output" format_source="infile" metadata_source="infile" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="sed1.txt" />
+            <param name="code" value="1d ; s/foo/bar/" />
+            <param name="silent" value="" />
+            <output name="output" file="sed_results1.txt" />
+        </test>
+        <test>
+            <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>
+<![CDATA[
+**What it does**
+
+This tool runs the unix **sed** command on the selected data file.
+
+.. class:: infomark
+
+**TIP:** This tool uses the **extended regular** expression syntax (same as running 'sed -r').
+
+
+
+**Further reading**
+
+- Short sed tutorial (http://www.linuxhowtos.org/System/sed_tutorial.htm)
+- Long sed tutorial (http://www.grymoire.com/Unix/Sed.html)
+- sed faq with good examples (http://sed.sourceforge.net/sedfaq.html)
+- sed cheat-sheet (http://www.catonmat.net/download/sed.stream.editor.cheat.sheet.pdf)
+- Collection of useful sed one-liners (http://student.northpark.edu/pemente/sed/sed1line.txt)
+
+-----
+
+**Sed commands**
+
+The most useful sed command is **s** (substitute).
+
+**Examples**
+
+- **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,}/--&--/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**
+
+The select tool searches the data for lines containing or not containing a match to the given pattern. A Regular Expression is a pattern descibing a certain amount of text.
+
+- **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
+- **^** matches the beginning of a string(but not an internal line).
+- **(** .. **)** groups a particular pattern.
+- **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
+
+  - **{n}** The preceding item is matched exactly n times.
+  - **{n,}** The preceding item ismatched n or more times.
+  - **{n,m}** The preceding item is matched at least n times but not more than m times.
+
+- **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**.
+- **.** Matches any single character except a newline.
+- ***** The preceding item will be matched zero or more times.
+- **?** The preceding item is optional and matched at most once.
+- **+** The preceding item will be matched one or more times.
+- **^** has two meaning:
+  - matches the beginning of a line or string.
+  - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
+- **$** matches the end of a line or string.
+- **\|** Separates alternate possibilities.
+
+
+**Note**: SED uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported.
+
+@REFERENCES@
+]]>
+    </help>
+</tool>