view concat.xml @ 4:35a89f8cc96e draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat commit 58cb53d87440bd45e014fb37cddc276dc79b9d94

<tool id="gops_concat_1" name="Concatenate" version="1.0.1">
    <description>two BED files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <code file="operation_filter.py"/>
    <command><![CDATA[
python '$__tool_directory__/gops_concat.py'
'$input1'
'$input2'
'$output'
-1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
-2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}
$sameformat
    ]]></command>
    <inputs>
        <param name="input1" type="data" format="interval" label="Concatenate" help="First dataset" />
        <param name="input2" type="data" format="interval" label="With" help="Second dataset" />
        <param name="sameformat" type="boolean" truevalue="--sameformat" falsevalue="" checked="true" label="Both datasets are in the same format?" help="If unchecked, Second dataset will be forced into the format of First dataset" />
    </inputs>
    <outputs>
        <data name="output" format_source="input1" metadata_source="input1" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="1.bed" />
            <param name="input2" value="2.bed" />
            <param name="sameformat" value="true" />
            <output name="output" file="gops_concat_out1.bed" />
        </test>
        <test>
            <param name="input1" value="1.bed" />
            <param name="input2" value="1.interval" />
            <param name="sameformat" value="false" />
            <output name="output" file="gops_concat_out2.bed" />
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**TIP:** If your dataset does not appear in the pulldown menu -> it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns.

@SCREENCASTS@

**Syntax**

- **Both datasets are exactly the same filetype** will preserve all extra fields in both files.  Leaving this unchecked will force the second dataset to use the same column assignments for chrom, start, end and strand, but will fill extra fields with a period(.).  In both cases, the output fields are truncated or padded with fields of periods to maintain a truly tabular output.

-----

**Example**

.. image:: gops_concatenate.gif
    ]]></help>
</tool>