comparison grep.xml @ 19:12615d397df7 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 70980e329cd9fa78e74bf14a76fd4ded9bd2b91f

18:d698c222f354

<tool id="tp_grep_tool" name="Search in textfiles" version="@BASE_VERSION@.1">
    <description>(grep)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="2.14">grep</requirement>
        <requirement type="package" version="4.4">sed</requirement><!-- for ansi2html.sh -->
    </requirements>
    <version_command>grep --version | head -n 1</version_command>
    <command>
<![CDATA[
        #if str($color) == "COLOR":

                $regex_type
                -A $lines_after
                -B $lines_before
                $invert
                $case_sensitive
                -- "${url_paste}"
                '${infile}' | $__tool_directory__/ansi2html.sh > "${output}"
        #else:
            grep
                $regex_type
                -A $lines_after
                -B $lines_before
                $invert
                $case_sensitive
                 -- "${url_paste}"
                '${infile}' | grep -v "^--$" > "${output}"
        #end if
]]>
    </command>
    <inputs>
        <param name="infile" format="txt" type="data" label="Select lines from" />

            <option value="">Match</option>
            <option value="-v">Don't Match</option>
        </param>

        <param name="regex_type" type="select" label="Type of regex">
            <option value="-G">Basic</option>
            <option value="-P" selected="true">Perl</option>
            <option value="-E">Extended (egrep)</option>
        </param>

        <param name="url_paste" type="text" label="Regular Expression" help="See below for more details">
            <sanitizer>
                <valid initial="string.printable">

            <param name="lines_before" value="0" />
            <param name="lines_after" value="0" />
            <param name="color" value="NOCOLOR" />
            <output name="output" file="egrep_results1.txt" />
        </test>
        <test><!-- same regex as egrep test, but different outcome with basic regex -->
            <param name="infile" value="egrep1.txt" />
            <param name="case_sensitive" value="case sensitive" />
            <param name="regex_type" value="-G" />
            <param name="invert" value="" />
            <param name="url_paste" value="[^ ]+" />
            <param name="lines_before" value="0" />
            <param name="lines_after" value="0" />
            <param name="color" value="NOCOLOR" />
            <output name="output" file="egrep_results2.txt" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

  - 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>
    <expand macro="citations" />
</tool>

19:12615d397df7

<tool id="tp_grep_tool" name="Search in textfiles" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>(grep)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creator"/>
    <requirements>
        <requirement type="package" version="3.11">grep</requirement>
        <requirement type="package" version="4.8">sed</requirement><!-- for ansi2html.sh -->
    </requirements>
    <version_command>grep --version | head -n 1</version_command>
    <command>
<![CDATA[
        #if str($color) == "COLOR":

                $regex_type
                -A $lines_after
                -B $lines_before
                $invert
                $case_sensitive
                -- '${url_paste}'
                '${infile}' | '$__tool_directory__/ansi2html.sh' > '${output}'
        #else:
            grep
                $regex_type
                -A $lines_after
                -B $lines_before
                $invert
                $case_sensitive
                 -- '${url_paste}'
                '${infile}' | grep -v "^--$" > '${output}'
        #end if
]]>
    </command>
    <inputs>
        <param name="infile" format="txt" type="data" label="Select lines from" />

            <option value="">Match</option>
            <option value="-v">Don't Match</option>
        </param>

        <param name="regex_type" type="select" label="Type of regex">
            <option value="-G">Basic (-G)</option>
            <option value="-P" selected="true">Perl (-P)</option>
            <option value="-E">Extended (egrep -E)</option>
        </param>

        <param name="url_paste" type="text" label="Regular Expression" help="See below for more details">
            <sanitizer>
                <valid initial="string.printable">

            <param name="lines_before" value="0" />
            <param name="lines_after" value="0" />
            <param name="color" value="NOCOLOR" />
            <output name="output" file="egrep_results1.txt" />
        </test>
        <test><!-- tests basic regex; + must be backslashed to match -->
            <param name="infile" value="egrep1.txt" />
            <param name="case_sensitive" value="case sensitive" />
            <param name="regex_type" value="-G" />
            <param name="invert" value="" />
            <param name="url_paste" value="[^ ]\+" />
            <param name="lines_before" value="0" />
            <param name="lines_after" value="0" />
            <param name="color" value="NOCOLOR" />
            <output name="output" file="egrep_results1.txt" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

  - 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.

]]>
    </help>
    <expand macro="citations" />
</tool>