comparison split_file_on_column.xml @ 2:90b52d8d6f2c draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_on_column commit 36d05738e78c68091b45779624734e6a47829856-dirty

1:0ba6d09a71d6

<tool id="tp_split_on_column" name="Split file" force_history_refresh="True" version="0.1.1">
    <description>according to the values of a column</description>
    <requirements>
        <requirement type="package" version="4.1.0">gnu_awk</requirement>
    </requirements>
    <command>
        awk -F'\t' '{print > "primary_${outfile.id}_" \$$column "_visible_${infile.ext}" }' $infile;
        echo 'Created' `ls -l | wc -l` 'files:' > $outfile;
        ls -1 --hide="*_stdout" --hide="*_stderr" >> $outfile;
    </command>

    <inputs>
        <param format="txt" name="infile" type="data" label="File to select" />
        <param name="column" label="on column" type="data_column" data_ref="infile" accept_default="true" />
    </inputs>

    <outputs>
        <data format="input" name="outfile" metadata_source="infile" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help>

**What it does**

This tool splits a file into different smaller files using a specific column. 
It will work like the group tool, but every group is saved to its own file.

-----

**Example**

Splitting on column 4 from this::

    chr7  56632  56652  cluster 1
    chr7  56736  56756  cluster 1
    chr7  56761  56781  cluster 2
    chr7  56772  56792  cluster 2

    chr7  56761  56781  cluster 2
    chr7  56772  56792  cluster 2
    chr7  56775  56795  cluster 2


    </help>
</tool>

2:90b52d8d6f2c

<tool id="tp_split_on_column" name="Split file" version="0.2">
    <description>according to the values of a column</description>
    <requirements>
        <requirement type="package" version="4.1.0">gnu_awk</requirement>
    </requirements>
    <command>
<![CDATA[
        awk -F'\t' '{print > \$$column ".$infile.ext" }' $infile
]]>
    </command>
    <inputs>
        <param format="tabular" name="infile" type="data" label="File to select" />
        <param name="column" label="on column" type="data_column" data_ref="infile" accept_default="true" />
    </inputs>
    <outputs>
        <collection name="split_output" type="list" label="Table split on first column">
            <discover_datasets pattern="__name_and_ext__" directory="." />
        </collection>
    </outputs>
    <!--outputs>
        <data format="input" name="outfile" metadata_source="infile" label="${tool.name} on ${on_string}"/>
    </outputs-->
    <tests>
        <test>
            <param name="infile" value="5cols.tabular" ftype="tabular"/>
            <param name="column" value="5" />
            <output_collection name="split_output" type="list">
                <element name="1">
                    <assert_contents>
                        <has_text_matching expression="chr7\t56632\t56652\tcluster\t1" />
                    </assert_contents>
                </element>
                <element name="2">
                    <assert_contents>
                        <has_text_matching expression="chr7\t56761\t56781\tcluster\t2" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help>
<![CDATA[

**What it does**

This tool splits a file into different smaller files using a specific column.
It will work like the group tool, but every group is saved to its own file.

-----

**Example**

Splitting on column 5 from this::

    chr7  56632  56652  cluster 1
    chr7  56736  56756  cluster 1
    chr7  56761  56781  cluster 2
    chr7  56772  56792  cluster 2

    chr7  56761  56781  cluster 2
    chr7  56772  56792  cluster 2
    chr7  56775  56795  cluster 2


]]>
    </help>
</tool>