comparison get_flanks.xml @ 4:077f404ae1bb draft default tip

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

3:4cd116158aef

<tool id="get_flanks1" name="Get flanks" version="1.0.0">
  <description>returns flanking region/s for every gene</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">get_flanks.py $input $out_file1 $size $direction $region -o $offset -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}</command>
  <inputs>
    <param format="interval" name="input" type="data" label="Select data"/>
    <param name="region" type="select" label="Region">
      <option value="whole" selected="true">Whole feature</option>
      <option value="start">Around Start</option>
      <option value="end">Around End</option>
    </param>
    <param name="direction" type="select" label="Location of the flanking region/s">
      <option value="Upstream">Upstream</option>
      <option value="Downstream">Downstream</option>
      <option value="Both">Both</option>
    </param>
    <param name="offset" type="integer" value="0" label="Offset" help="Use positive values to offset co-ordinates in the direction of transcription and negative values to offset in the opposite direction."/>
    <param name="size" type="integer" value="50" label="Length of the flanking region(s)" help="Use non-negative value for length"/>
    
    
  </inputs>
  <outputs>
    <data format="interval" name="out_file1" metadata_source="input"/>
  </outputs>
  <tests>
    <test>
      <param name="input" value="flanks_inp.bed"/>
      <param name="offset" value="-500"/>
      <param name="size" value="1000"/>
      <param name="direction" value="Both"/>
      <param name="region" value="whole"/>
      <output name="out_file1" file="flanks_out1.bed"/>
    </test>
    <test>
      <param name="input" value="flanks_inp.bed"/>
      <param name="offset" value="200"/>
      <param name="size" value="1000"/>
      <param name="direction" value="Downstream"/>
      <param name="region" value="start" />
      <output name="out_file1" file="flanks_out2.bed"/>
    </test>
  </tests>
 <help> 

This tool finds the upstream and/or downstream flanking region(s) of all the selected regions in the input file. 

**Note:** Every line should contain at least 3 columns: Chromosome number, Start and Stop co-ordinates. If any of these columns is missing or if start and stop co-ordinates are not numerical, the tool may encounter exceptions and such lines are skipped as invalid. The number of invalid skipped lines is documented in the resulting history item as a "Data issue".

-----


**Example 1**

- For the following dataset::

- running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Dataset negative strand; Magenta: Flanks output)**::

   chr22  500  800  NM_028946 0 -

.. image:: flanks_ex2.gif

</help>  


</tool>

4:077f404ae1bb

<tool id="get_flanks1" name="Get flanks" version="1.0.0">
    <description>returns flanking region/s for every gene</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command><![CDATA[
python '$__tool_directory__/get_flanks.py'
'$input'
'$out_file1'
$size
$direction
$region
-o $offset
-l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}
    ]]></command>
    <inputs>
        <param name="input" type="data" format="interval" label="Select data"/>
        <param name="region" type="select" label="Region">
            <option value="whole" selected="true">Whole feature</option>
            <option value="start">Around Start</option>
            <option value="end">Around End</option>
        </param>
        <param name="direction" type="select" label="Location of the flanking region/s">
            <option value="Upstream">Upstream</option>
            <option value="Downstream">Downstream</option>
            <option value="Both">Both</option>
        </param>
        <param name="offset" type="integer" value="0" label="Offset" help="Use positive values to offset co-ordinates in the direction of transcription and negative values to offset in the opposite direction."/>
        <param name="size" type="integer" value="50" label="Length of the flanking region(s)" help="Use non-negative value for length"/>
    </inputs>
    <outputs>
        <data name="out_file1" format_source="input" metadata_source="input"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="flanks_inp.bed"/>
            <param name="offset" value="-500"/>
            <param name="size" value="1000"/>
            <param name="direction" value="Both"/>
            <param name="region" value="whole"/>
            <output name="out_file1" file="flanks_out1.bed"/>
        </test>
        <test>
            <param name="input" value="flanks_inp.bed"/>
            <param name="offset" value="200"/>
            <param name="size" value="1000"/>
            <param name="direction" value="Downstream"/>
            <param name="region" value="start" />
            <output name="out_file1" file="flanks_out2.bed"/>
        </test>
    </tests>
    <help><![CDATA[
This tool finds the upstream and/or downstream flanking region(s) of all the selected regions in the input file.

**Note:** Every line should contain at least 3 columns: Chromosome number, Start and Stop co-ordinates. If any of these columns is missing or if start and stop co-ordinates are not numerical, the tool may encounter exceptions and such lines are skipped as invalid. The number of invalid skipped lines is documented in the resulting history item as a "Data issue".

-----

**Example 1**

- For the following dataset::

- running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Dataset negative strand; Magenta: Flanks output)**::

   chr22  500  800  NM_028946 0 -

.. image:: flanks_ex2.gif
    ]]></help>
</tool>