view complement.xml @ 3:48d2f6a56a90 draft

planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

<tool id="gops_complement_1" name="Complement" version="1.0.0">
  <description>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_complement.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -l ${chromInfo} $allchroms</command>
  <inputs>
    <param format="interval" name="input1" type="data">
      <label>Complement regions of</label>
    </param>
    <param name="allchroms" type="boolean" truevalue="--all" falsevalue="" label="Genome-wide complement">
    </param>
   </inputs>
  <outputs>
    <data format="input" name="output" metadata_source="input1" />
  </outputs>
  <code file="operation_filter.py"/>
  <tests>
    <test>
      <param name="input1" value="1.bed" dbkey="hg17" />
      <param name="allchroms" value="true" />
      <output name="output" file="gops_complement_out.bed" />
    </test>
    <test>
      <param name="input1" value="2_mod.bed" ftype="interval" dbkey="hg17" />
      <param name="allchroms" value="true" />
      <output name="output" file="gops_complement_out_diffCols.dat" />
    </test>
    <test>
      <param name="input1" value="gops_bigint.interval" dbkey="hg17" />
      <param name="allchroms" value="true" />
      <output name="output" file="gops_complement_out2.bed" />
    </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.

This operation complements the regions of a set of intervals.  Regions are returned that represent the empty space in the input interval.

-----

**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

-----

**Syntax**

- **Genome-wide complement** will complement all chromosomes of the genome.  Leaving this option unchecked will only complement chromosomes present in the dataset.

-----

**Example**

.. image:: gops_complement.gif

</help>
</tool>