annotate tools/filters/catWrapper.xml @ 1:cdcb0ce84a1b

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<tool id="cat1" name="Concatenate datasets">
    <description>tail-to-head</description>
    <command interpreter="python">
        catWrapper.py 
        $out_file1 
        $input1
        #for $q in $queries
            ${q.input2}
        #end for
    </command>
    <inputs>
        <param name="input1" type="data" label="Concatenate Dataset"/>
        <repeat name="queries" title="Dataset">
            <param name="input2" type="data" label="Select" />
        </repeat>
    </inputs>
    <outputs>
        <data name="out_file1" format="input" metadata_source="input1"/>
    </outputs>
    <tests>
        <test>
            <param name="input1" value="1.bed"/>
            <param name="input2" value="2.bed"/>
            <output name="out_file1" file="cat_wrapper_out1.bed"/>
        </test>
        <!--TODO: if possible, enhance the underlying test code to handle this test
            the problem is multiple params with the same name "input2"
        <test>
            <param name="input1" value="1.bed"/>
            <param name="input2" value="2.bed"/>
            <param name="input2" value="3.bed"/>
            <output name="out_file1" file="cat_wrapper_out2.bed"/>
        </test>
        -->
    </tests>
    <help>

.. class:: warningmark

**WARNING:** Be careful not to concatenate datasets of different kinds (e.g., sequences with intervals). This tool does not check if the datasets being concatenated are in the same format. 

-----

**What it does**

Concatenates datasets

-----

**Example**

Concatenating Dataset::

    chrX  151087187  151087355  A  0  -
    chrX  151572400  151572481  B  0  +

with Dataset1::

    chr1  151242630  151242955  X  0  +
    chr1  151271715  151271999  Y  0  +
    chr1  151278832  151279227  Z  0  -
    
and with Dataset2::

    chr2  100000030  200000955  P  0  +
    chr2  100000015  200000999  Q  0  +

will result in the following::

    chrX  151087187  151087355  A  0  -
    chrX  151572400  151572481  B  0  +
    chr1  151242630  151242955  X  0  +
    chr1  151271715  151271999  Y  0  +
    chr1  151278832  151279227  Z  0  -
    chr2  100000030  200000955  P  0  +
    chr2  100000015  200000999  Q  0  +

    </help>
</tool>