annotate cat.xml @ 3:37e1eb05b1b4 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty

<tool id="tp_cat" name="Concatenate datasets" version="0.1.0">
    <description>tail-to-head (cat)</description>
    <requirements>
        <requirement type="package" version="8.22">gnu_coreutils</requirement>
    </requirements>
    <version_command>
    <![CDATA[
        cat --version | head -n 1
    ]]>
    </version_command>
    <command>
    <![CDATA[
        cat
            #echo ' '.join(['"%s"' % $file for $file in $inputs])#
            #for $q in $queries:
                #echo ' '.join(['"%s"' % $file for $file in $q.inputs2])#
            #end for
        > $out_file1
    ]]></command>
    <inputs>
        <param name="inputs" multiple="true" type="data" format="txt" label="Datasets to concatenate"/>
        <repeat name="queries" title="Dataset">
            <param name="inputs2" type="data" format="txt" multiple="True" label="Select" />
        </repeat>
    </inputs>
    <outputs>
        <data name="out_file1" format_source="inputs" metadata_source="inputs"/>
    </outputs>
    <tests>
        <test>
            <param name="inputs" value="sort_result1.bed,sort_result2.bed,sort_result3.bed"/>
            <output name="out_file1" file="cat_result1.txt"/>
        </test>
        <test>
            <param name="inputs" value="sort_result1.bed,sort_result3.bed"/>
            <repeat name="queries">
                <param name="inputs2" value="sort_result3.bed,sort_result3.bed"/>
            </repeat>
            <repeat name="queries">
                <param name="inputs2" value="sort_result3.bed"/>
            </repeat>
            <output name="out_file1" file="cat_result2.txt"/>
        </test>
    </tests>
    <help>
<![CDATA[

.. 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>