comparison replace_text_in_column.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_replace_in_column" name="Replace Text" version="@BASE_VERSION@.3">
    <description>in a specific column</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

            '{ 
            #for $replacement in $replacements:
                \$$replacement.column = gensub( /$replacement.find_pattern/, "$replacement.replace_pattern", "g", \$$replacement.column ) ;
            #end for
            print \$0 ; }'
            "$infile"
        > "$outfile"
]]>
    </command>
    <inputs>
        <param format="tabular" name="infile" type="data" label="File to process" />
        <repeat name="replacements" title="Replacement" min="1">

- **\|** Separates alternate possibilities.


**Note**: AWK uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported.

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

19:12615d397df7

<tool id="tp_replace_in_column" name="Replace Text" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>in a specific column</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creator"/>
    <requirements>
        <requirement type="package" version="5.3.0">gawk</requirement>
    </requirements>
    <version_command>awk --version | head -n 1</version_command>
    <command>
<![CDATA[
        awk

            '{ 
            #for $replacement in $replacements:
                \$$replacement.column = gensub( /$replacement.find_pattern/, "$replacement.replace_pattern", "g", \$$replacement.column ) ;
            #end for
            print \$0 ; }'
            '$infile'
        > '$outfile'
]]>
    </command>
    <inputs>
        <param format="tabular" name="infile" type="data" label="File to process" />
        <repeat name="replacements" title="Replacement" min="1">

- **\|** Separates alternate possibilities.


**Note**: AWK uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported.

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