comparison merge.xml @ 4:381cd27bf67a draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689

3:0926c81f382c

<tool id="gops_merge_1" name="Merge" version="1.0.0">
  <description>the overlapping intervals of a dataset</description>
  <requirements>
    <requirement type="package" version="0.7.1">bx-python</requirement>
    <requirement type="package" version="1.0.0">galaxy-ops</requirement>
  </requirements>
  <command interpreter="python">gops_merge.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} $returntype</command>
  <inputs>
    <param format="interval" name="input1" type="data">
      <label>Merge overlaping regions of</label>
    </param>
    <param name="returntype" type="boolean" truevalue="-3" falsevalue="">
      <label>Output 3 column bed</label>
    </param>
   </inputs>
  <outputs>
    <data format="input" name="output" metadata_source="input1" />
  </outputs>
  <code file="operation_filter.py">
    <hook exec_after_process="exec_after_merge" />
  </code>
  <tests>
    <test>
      <param name="input1" value="1.bed" />
      <output name="output" file="gops-merge.dat" />
      <param name="returntype" value="true" />
    </test>
    <test>
      <param name="input1" value="2_mod.bed" ftype="interval"/>
      <output name="output" file="gops_merge_diffCols.dat" />
      <param name="returntype" value="true" />
    </test>
    <test>
      <param name="input1" value="gops_bigint.interval" />
      <output name="output" file="gops_merge_out2.bed" />
      <param name="returntype" value="true" />
    </test>
  </tests>
  <help>

.. class:: infomark

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

-----

**Screencasts!**

See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).

.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations

-----

This operation merges all overlapping intervals into single intervals.

**Example**

.. image:: gops_merge.gif

</help>
</tool>

4:381cd27bf67a

<tool id="gops_merge_1" name="Merge" version="1.0.0">
    <description>the overlapping intervals of a dataset</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <code file="operation_filter.py">
        <hook exec_after_process="exec_after_merge" />
    </code>
    <command><![CDATA[
python '$__tool_directory__/gops_merge.py'
'$input1'
'$output'
-1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
$returntype
    ]]></command>
    <inputs>
        <param name="input1" type="data" format="interval" label="Merge overlapping regions of" />
        <param name="returntype" type="boolean" truevalue="-3" falsevalue="" label="Output 3 column bed" />
    </inputs>
    <outputs>
        <data name="output" format_source="input1" metadata_source="input1" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="1.bed" />
            <param name="returntype" value="true" />
            <output name="output" file="gops-merge.dat" />
        </test>
        <test>
            <param name="input1" value="2_mod.bed" ftype="interval"/>
            <param name="returntype" value="true" />
            <output name="output" file="gops_merge_diffCols.dat" />
        </test>
        <test>
            <param name="input1" value="gops_bigint.interval" />
            <param name="returntype" value="true" />
            <output name="output" file="gops_merge_out2.bed" />
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

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

@SCREENCASTS@

This operation merges all overlapping intervals into single intervals.

**Example**

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