diff grep.xml @ 0:5314e5d6f040 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/grep.xml	Thu Jan 29 07:53:17 2015 -0500
@@ -0,0 +1,165 @@
+<tool id="tp_grep_tool" name="Search in textfiles" version="@BASE_VERSION@.0">
+    <description>(grep)</description>
+    <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>
+    </expand>
+    <version_command>grep --version | head -n 1</version_command>
+    <command>
+<![CDATA[
+        #if str($color) == "COLOR":
+            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
+                -A $lines_after
+                -B $lines_before
+                $invert
+                $case_sensitive
+                 -- "${url_paste}"
+                '${infile}' | grep -v "^--$" > "${output}"
+        #end if
+
+        ##grep_wrapper.sh '$infile' '$output' '$url_paste' $color -A $lines_after -B $lines_before $invert $case_sensitive
+]]>
+    </command>
+    <inputs>
+        <param name="infile" format="txt" type="data" label="Select lines from" />
+
+        <param name="invert" type="select" label="that">
+            <option value="">Match</option>
+            <option value="-v">Don't Match</option>
+        </param>
+
+        <param name="url_paste" type="text" size="40" label="Regular Expression" help="See below for more details">
+            <sanitizer>
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+        </param>
+
+        <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" 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 name="output" format_source="infile" 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="grep1.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="grep_results1.txt" />
+        </test>
+        <test>
+            <!-- grep a FASTA file for sequences with specific motif -
+             show highlighed output -->
+            <param name="infile" value="grep1.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="grep_results2.html" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+This tool runs the unix **grep** command on the selected data file.
+
+.. class:: infomark
+
+**TIP:** This tool uses the **perl** regular expression syntax (same as running 'grep -P'). This is **NOT** the POSIX or POSIX-extended syntax (unlike the awk/sed tools).
+
+
+**Further reading**
+
+- Wikipedia's Regular Expression page (http://en.wikipedia.org/wiki/Regular_expression)
+- Regular Expressions cheat-sheet (PDF) (http://www.addedbytes.com/cheat-sheets/download/regular-expressions-cheat-sheet-v2.pdf)
+- Grep Tutorial (http://www.panix.com/~elflord/unix/grep.html)
+
+-----
+
+**Grep Examples**
+
+- **AGC.AAT** would match lines with AGC followed by any character, followed by AAT (e.g. **AGCQAAT**, **AGCPAAT**, **AGCwAAT**)
+- **C{2,5}AGC** would match lines with 2 to 5 consecutive Cs followed by AGC
+- **TTT.{4,10}AAA** would match lines with 3 Ts, followed by 4 to 10 characters (any characeters), followed by 3 As.
+- **^chr([0-9A-Za-z])+** would match lines that begin with chromsomes, such as lines in a BED format file.
+- **(ACGT){1,5}** would match at least 1 "ACGT" and at most 5 "ACGT" consecutively.
+- **hsa|mmu** would match lines containing "hsa" or "mmu" (or both).
+
+-----
+
+**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.
+
+- **( ) { } [ ] . * ? + \ ^ $** are all special characters. **\\** can be used to "escape" a special character, allowing that special character to be searched for.
+- **^** matches the beginning of a string(but not an internal line).
+- **\\d** matches a digit, same as [0-9].
+- **\\D** matches a non-digit.
+- **\\s** matches a whitespace character.
+- **\\S** matches anything BUT a whitespace.
+- **\\t** matches a tab.
+- **\\w** matches an alphanumeric character ( A to Z, 0 to 9 and underscore )
+- **\\W** matches anything but an alphanumeric character.
+- **(** .. **)** groups a particular pattern.
+- **\\Z** matches the end of a string(but not a internal line).
+- **{** n or n, or n,m **}** specifies an expected number of repetitions of the preceding pattern.
+
+  - **{n}** The preceding item is matched exactly n times.
+  - **{n,}** The preceding item ismatched n or more times.
+  - **{n,m}** The preceding item is matched at least n times but not more than m times.
+
+- **[** ... **]** creates a character class. Within the brackets, single characters can be placed. A dash (-) may be used to indicate a range such as **a-z**.
+- **.** Matches any single character except a newline.
+- ***** The preceding item will be matched zero or more times.
+- **?** The preceding item is optional and matched at most once.
+- **+** The preceding item will be matched one or more times.
+- **^** has two meaning:
+  - matches the beginning of a line or string.
+  - indicates negation in a character class. For example, [^...] matches every character except the ones inside brackets.
+- **$** matches the end of a line or string.
+- **\|** Separates alternate possibilities.
+
+@REFERENCES@
+]]>
+    </help>
+</tool>