comparison replace_text_in_column.xml @ 12:a6f147a050a2 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit f47799941f9e11c313b38758bfdaab0ce83844f8

11:74a8bef53a00

<tool id="tp_replace_in_column" name="Replace Text" version="@BASE_VERSION@.2">
    <description>in a specific column</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>

<![CDATA[
        awk
            -v OFS="\t"
            -v FS="\t"
            --re-interval
            --sandbox '{ \$$column = gensub( /$find_pattern/, "$replace_pattern", "g", \$$column ) ; print \$0 ; }'
            "$infile"
        > "$outfile"
]]>
    </command>
    <inputs>
        <param format="tabular" name="infile" type="data" label="File to process" />
        <param name="column" label="in column" type="data_column" data_ref="infile" accept_default="true" />

        <param name="find_pattern" type="text" 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" 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_column1.txt" ftype="tabular" />
              <param name="column" value="4" />
              <param name="find_pattern" value=".+_(R.)" />
              <param name="replace_pattern" value="\\1" />
              <output name="outfile" file="replace_text_in_column_results1.txt" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

12:a6f147a050a2

<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>

<![CDATA[
        awk
            -v OFS="\t"
            -v FS="\t"
            --re-interval
            --sandbox 
            '{ 
            #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">
            <param name="column" label="in column" type="data_column" data_ref="infile" accept_default="true" />

            <param name="find_pattern" type="text" 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" 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>
        </repeat>
    </inputs>
    <outputs>
        <data name="outfile" format_source="infile" metadata_source="infile" />
    </outputs>
    <tests>
        <test>
              <param name="infile" value="replace_text_in_column1.txt" ftype="tabular" />
              <param name="column" value="4" />
              <param name="find_pattern" value=".+_(R.)" />
              <param name="replace_pattern" value="\\1" />
              <output name="outfile" file="replace_text_in_column_results1.txt" />
        </test>
        <test>
              <param name="infile" value="replace_text_in_column1.txt" ftype="tabular" />
              <repeat name="replacements">
                <param name="column" value="1" />
                <param name="find_pattern" value="[a-z]{2}([a-z])" />
                <param name="replace_pattern" value="\\1" />
              </repeat>
              <repeat name="replacements">
                <param name="column" value="4" />
                <param name="find_pattern" value=".+_(R.)" />
                <param name="replace_pattern" value="\\1" />
              </repeat>
              <output name="outfile" file="replace_text_in_column_results2.txt" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**