diff replace_text_in_line.xml @ 0:5314e5d6f040 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/replace_text_in_line.xml	Thu Jan 29 07:53:17 2015 -0500
@@ -0,0 +1,132 @@
+<tool id="tp_replace_in_line" name="Replace Text" version="@BASE_VERSION@.0">
+    <description>in entire line</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
+            -r
+            --sandbox
+            "s/$find_pattern/$replace_pattern/g"
+            "$infile"
+        > "$outfile"
+]]>
+    </command>
+    <inputs>
+        <param format="txt" name="infile" type="data" label="File to process" />
+         <param name="find_pattern" type="text" size="20" label="Find pattern" help="Use simple text, or a valid regular expression (without backslashes // ) " >
+            <sanitizer>
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+         <param name="replace_pattern" type="text" size="20" label="Replace with:" help="Use simple text, or &amp; (ampersand) and \\1 \\2 \\3 to refer to matched text. See examples below." >
+            <sanitizer>
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="outfile" format_source="infile" metadata_source="infile"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="replace_text_in_line1.txt" />
+            <param name="find_pattern" value="CTC." />
+            <param name="replace_pattern" value="FOOBAR" />
+            <output name="outfile" file="replace_text_in_line_results1.txt" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+This tool performs find & replace operation on a specified file.
+
+.. class:: infomark
+
+The **pattern to find** uses the **extended regular** expression syntax (same as running 'sed -r').
+
+.. class:: infomark
+
+**TIP:** If you need more complex patterns, use the *sed* tool.
+
+-----
+
+**Examples of Find Patterns**
+
+- **HELLO**     The word 'HELLO' (case sensitive).
+- **AG.T**      The letters A,G followed by any single character, followed by the letter T.
+- **A{4,}**     Four or more consecutive A's.
+- **chr2[012]\\t**       The words 'chr20' or 'chr21' or 'chr22' followed by a tab character.
+- **hsa-mir-([^ ]+)**        The text 'hsa-mir-' followed by one-or-more non-space characters. When using parenthesis, the matched content of the parenthesis can be accessed with **\1** in the **replace** pattern.
+
+
+**Examples of Replace Patterns**
+
+- **WORLD**  The word 'WORLD' will be placed whereever the find pattern was found.
+- **FOO-&-BAR**  Each time the find pattern is found, it will be surrounded with 'FOO-' at the begining and '-BAR' at the end. **$** (ampersand) represents the matched find pattern.
+- **\\1**   The text which matched the first parenthesis in the Find Pattern.
+
+
+-----
+
+**Example 1**
+
+**Find Pattern:** HELLO
+**Replace Pattern:** WORLD
+
+Every time the word HELLO is found, it will be replaced with the word WORLD.
+
+
+-----
+
+**Example 2**
+
+**Find Pattern:** ^(.{4})
+**Replace Pattern:** &\\t
+
+Find the first four characters in each line, and replace them with the same text, followed by a tab character. In practice - this will split the first line into two columns.
+
+
+-----
+
+**Extened 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>