comparison subtract.xml @ 5:0145969324c4 draft

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

4:7a2a604ae9c8

<tool id="gops_subtract_1" name="Subtract" version="1.0.0">
  <description>the intervals of two datasets</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_subtract.py 
      $input1 $input2 $output

      #if isinstance( $input1.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__):
        -1 1,4,5,7 --gff1
      #else:
        -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
      #end if

      #if isinstance( $input2.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__):
        -2 1,4,5,7 --gff2
      #else:
          -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol} 
      #end if

      -m $min $returntype
  </command>
  <inputs>
    <param format="interval,gff" name="input2" type="data" help="Second dataset">
      <label>Subtract</label>
    </param>

    <param format="interval,gff" name="input1" type="data" help="First dataset">
      <label>from</label>
    </param>

    <param name="returntype" type="select" label="Return" help="of the first dataset (see figure below)">
      <option value="">Intervals with no overlap</option>
      <option value="-p">Non-overlapping pieces of intervals</option>
    </param>
    
    <param name="min" type="integer" value="1" min="1" help="(bp)">
      <label>where minimal overlap is</label>
    </param>
   </inputs>
  <outputs>
    <data format="input" name="output" metadata_source="input1"/>
  </outputs>
  <code file="operation_filter.py"/>
  <trackster_conf/>
  <tests>
    <test>
      <param name="input1" value="1.bed" />
      <param name="input2" value="2.bed" />
      <param name="min" value="1" />
      <param name="returntype" value="" />
      <output name="output" file="gops-subtract.dat" />
    </test>
    <test>
      <param name="input1" value="1.bed" />
      <param name="input2" value="2_mod.bed" ftype="interval"/>
      <param name="min" value="1" />
      <param name="returntype" value="" />
      <output name="output" file="gops_subtract_diffCols.dat" />
    </test>
    <test>
      <param name="input1" value="gops_subtract_bigint.bed" />
      <param name="input2" value="2.bed" />
      <param name="min" value="1" />
      <param name="returntype" value="" />
      <output name="output" file="gops-subtract.dat" />
    </test>
    <test>
      <param name="input1" value="1.bed" />
      <param name="input2" value="2.bed" />
      <param name="min" value="10" />
      <param name="returntype" value="Non-overlapping pieces of intervals" />
      <output name="output" file="gops-subtract-p.dat" />     
    </test>
    <!-- Subtract two GFF files. -->
    <test>
        <param name="input1" value="gops_subtract_in1.gff" />
        <param name="input2" value="gops_subtract_in2.gff" />
        <param name="min" value="1" />
        <param name="returntype" value="" />
        <output name="output" file="gops_subtract_out1.gff" />
    </test>
    <!-- Subtract BED file from GFF file. -->
    <test>
        <param name="input1" value="gops_subtract_in1.gff" />
        <param name="input2" value="gops_subtract_in2.bed" />
        <param name="min" value="1" />
        <param name="returntype" value="" />
        <output name="output" file="gops_subtract_out1.gff" />
    </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

-----

**Syntax**

- **Where overlap is at least** sets the minimum length (in base pairs) of overlap between elements of the two datasets.
- **Intervals with no overlap** returns entire intervals from the first dataset that do not overlap the second dataset.  The returned intervals are completely unchanged, and this option only filters out intervals that overlap with the second dataset.

.. image:: gops_subtractOverlappingIntervals.gif

Non-overlapping pieces of intervals:

.. image:: gops_subtractOverlappingPieces.gif

</help>
</tool>

5:0145969324c4

<tool id="gops_subtract_1" name="Subtract" version="1.0.0">
    <description>the intervals of two datasets</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <code file="operation_filter.py"/>
    <command><![CDATA[
python '$__tool_directory__/gops_subtract.py'
'$input1'
'$input2'
'$output'

#if $input1.is_of_type('gff')
    -1 1,4,5,7 --gff1
#else:
    -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
#end if

#if $input2.is_of_type('gff')
    -2 1,4,5,7 --gff2
#else:
    -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}
#end if

-m $min
$returntype
    ]]></command>
    <inputs>
        <param name="input2" type="data" format="interval,gff" label="Subtract" help="Second dataset" />
        <param name="input1" type="data" format="interval,gff" label="from" help="First dataset" />
        <param name="returntype" type="select" label="Return" help="of the first dataset (see figure below)">
            <option value="">Intervals with no overlap</option>
            <option value="-p">Non-overlapping pieces of intervals</option>
        </param>
        <param name="min" type="integer" value="1" min="1" label="where minimal overlap is" help="(bp)" />
    </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="min" value="1" />
            <param name="returntype" value="" />
            <output name="output" file="gops-subtract.dat" />
        </test>
        <test>
            <param name="input1" value="1.bed" />
            <param name="input2" value="2_mod.bed" ftype="interval"/>
            <param name="min" value="1" />
            <param name="returntype" value="" />
            <output name="output" file="gops_subtract_diffCols.dat" />
        </test>
        <test>
            <param name="input1" value="gops_subtract_bigint.bed" />
            <param name="input2" value="2.bed" />
            <param name="min" value="1" />
            <param name="returntype" value="" />
            <output name="output" file="gops-subtract.dat" />
        </test>
        <test>
            <param name="input1" value="1.bed" />
            <param name="input2" value="2.bed" />
            <param name="min" value="10" />
            <param name="returntype" value="Non-overlapping pieces of intervals" />
            <output name="output" file="gops-subtract-p.dat" />
        </test>
        <!-- Subtract two GFF files. -->
        <test>
            <param name="input1" value="gops_subtract_in1.gff" />
            <param name="input2" value="gops_subtract_in2.gff" />
            <param name="min" value="1" />
            <param name="returntype" value="" />
            <output name="output" file="gops_subtract_out1.gff" />
        </test>
        <!-- Subtract BED file from GFF file. -->
        <test>
            <param name="input1" value="gops_subtract_in1.gff" />
            <param name="input2" value="gops_subtract_in2.bed" />
            <param name="min" value="1" />
            <param name="returntype" value="" />
            <output name="output" file="gops_subtract_out1.gff" />
        </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@

**Syntax**

- **Where overlap is at least** sets the minimum length (in base pairs) of overlap between elements of the two datasets.
- **Intervals with no overlap** returns entire intervals from the first dataset that do not overlap the second dataset.  The returned intervals are completely unchanged, and this option only filters out intervals that overlap with the second dataset.

.. image:: gops_subtractOverlappingIntervals.gif

Non-overlapping pieces of intervals:

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