comparison awk.xml @ 11:74a8bef53a00 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 0ba37c1f33eeb1c77b4d9363d681fe522d9f7fe7

10:e39fceb6ab85

<tool id="tp_awk_tool" name="Text reformatting" version="@BASE_VERSION@.0">
    <description>with awk</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="4.1.3">gawk</requirement>
    </requirements>
    <version_command>awk --version | head -n 1</version_command>
    <command>
<![CDATA[
        awk

- **$2 == "chr3"**  will match lines whose second column is the string 'chr3'
- **$5-$4>23**  will match lines that after subtracting the value of the fourth column from the value of the fifth column, gives value alrger than 23.
- **/AG..AG/** will match lines that contain the regular expression **AG..AG** (meaning the characeters AG followed by any two characeters followed by AG). (This is the way to specify regular expressions on the entire line, similar to GREP.)
- **$7 ~ /A{4}U/**  will match lines whose seventh column contains 4 consecutive A's followed by a U. (This is the way to specify regular expressions on a specific field.)
- **10000 < $4 && $4 < 20000** will match lines whose fourth column value is larger than 10,000 but smaller than 20,000
- **BEGIN** will be executed once only, before the first input record is read. 
- If no pattern is specified, all lines match (meaning the **action** part will be executed on all lines).



**Action Examples**

11:74a8bef53a00

<tool id="tp_awk_tool" name="Text reformatting" version="@BASE_VERSION@.1">
    <description>with awk</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="4.2.0">gawk</requirement>
    </requirements>
    <version_command>awk --version | head -n 1</version_command>
    <command>
<![CDATA[
        awk

- **$2 == "chr3"**  will match lines whose second column is the string 'chr3'
- **$5-$4>23**  will match lines that after subtracting the value of the fourth column from the value of the fifth column, gives value alrger than 23.
- **/AG..AG/** will match lines that contain the regular expression **AG..AG** (meaning the characeters AG followed by any two characeters followed by AG). (This is the way to specify regular expressions on the entire line, similar to GREP.)
- **$7 ~ /A{4}U/**  will match lines whose seventh column contains 4 consecutive A's followed by a U. (This is the way to specify regular expressions on a specific field.)
- **10000 < $4 && $4 < 20000** will match lines whose fourth column value is larger than 10,000 but smaller than 20,000
- **BEGIN** will be executed once only, before the first input record is read.
- If no pattern is specified, all lines match (meaning the **action** part will be executed on all lines).



**Action Examples**