comparison awk.xml @ 29:4f7cade041cb draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 4dd118c84ed4d6157303e71438c24446ec4b4f31

28:e8b38ade9b3e

        env -i
        \$(which awk)
            --sandbox
            -v FS='	'
            -v OFS='	'
            --re-interval
            -f '$awk_script'
            '$infile'
        > '$outfile'
]]>

                <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="awk1.txt" />
            <!-- commas are not allowed in a value field. Values with comma will be splitted -->
            <param name="code" value='$2>0.5 { print $2*9"\t"$1 }' />
            <output name="outfile" file="awk_results1.txt" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Most AWK programs consist of **patterns** (i.e. rules that match lines of text) and **actions** (i.e. commands to execute when a pattern matches a line).

The basic form of AWK program is::

    pattern { action 1; action 2; action 3; }


**Pattern Examples**

- **$2 == "chr3"**  will match lines whose second column is the string 'chr3'

29:4f7cade041cb

        env -i
        \$(which awk)
            --sandbox
            -v FS='	'
            -v OFS='	'
            #for $i, $r in enumerate($variables, start=1)
                -v VAR$i='$r.value'
            #end for
            --re-interval
            -f '$awk_script'
            '$infile'
        > '$outfile'
]]>

                <valid initial="string.printable">
                    <remove value="&apos;"/>
                </valid>
            </sanitizer>
        </param>
        <repeat name="variables" min="0" default="0" title="Variables">
            <param name="value" type="text" label="Value">
                <validator type="regex">[a-zA-Z0-9 .]+</validator>
            </param>
        </repeat>
    </inputs>
    <outputs>
        <data name="outfile" format_source="infile" metadata_source="infile"/>
    </outputs>
    <tests>
        <test>
            <param name="infile" value="awk1.txt"/>
            <!-- commas are not allowed in a value field. Values with comma will be splitted -->
            <param name="code" value='$2>0.5 { print $2*9"\t"$1 }' />
            <output name="outfile" file="awk_results1.txt" />
        </test>
        <test>
            <param name="infile" value="awk1.txt"/>
            <!-- commas are not allowed in a value field. Values with comma will be splitted -->
            <param name="code" value='$2>VAR2 { print VAR1"\t"$2*9"\t"$1 }' />
            <repeat name="variables">
                <param name="value" value="xyz"/>
            </repeat>
            <repeat name="variables">
                <param name="value" value="0.1"/>
            </repeat>
            <output name="outfile">
                <assert_contents>
                    <has_line_matching expression="^xyz.*" n="6"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Most AWK programs consist of **patterns** (i.e. rules that match lines of text) and **actions** (i.e. commands to execute when a pattern matches a line).

The basic form of AWK program is::

    pattern { action 1; action 2; action 3; }

**Variables**

In order to allow parametrization in workflows, the tool allows to specify values for variables that can be used in AWK program.
that will be named **VAR1**, **VAR2**, ...


**Pattern Examples**

- **$2 == "chr3"**  will match lines whose second column is the string 'chr3'