annotate cat.xml @ 17:f46f0e4f75c4 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 5f5d5802a961a77ceb092cbdef90d93e29717029-dirty"

<tool id="tp_cat" name="Concatenate datasets" version="0.1.1">
    <description>tail-to-head (cat)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <version_command>
    <![CDATA[
        cat --version | head -n 1
    ]]>
    </version_command>
    <command>
    <![CDATA[
            #for $file in $inputs:
                cat '$file' >> '$out_file1' &&
            #end for
            #for $q in $queries:
                #for $file in $q.inputs2:
                    cat '$file' >> '$out_file1' &&
                #end for
            #end for
            exit 0
    ]]></command>
    <inputs>
        <param name="inputs" multiple="true" type="data" format="txt,fastq.gz,fasta.gz,genbank.gz,tabular.gz" label="Datasets to concatenate"/>
        <repeat name="queries" title="Dataset">
            <param name="inputs2" type="data" format="txt,fastq.gz,fasta.gz,genbank.gz,tabular.gz" 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  +

@REFERENCES@
]]>
    </help>
    <expand macro="citations" />
</tool>