comparison intersect.xml @ 5:60925436ca5f draft default tip

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

4:21717d77aee5

<tool id="gops_intersect_1" name="Intersect" 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_intersect.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 name="returntype" type="select" label="Return" help="(see figure below)">
          <option value="">Overlapping Intervals</option>
          <option value="-p">Overlapping pieces of Intervals</option>
      </param>
      <param format="interval,gff" name="input1" type="data" help="First dataset">
          <label>of</label>
      </param>
      <param format="interval,gff" name="input2" type="data" help="Second dataset">
          <label>that intersect</label>
      </param>
      <param name="min" type="integer" value="1" min="1" help="(bp)">
          <label>for at least</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_intersect_out.bed" />
    </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_intersect_diffCols.bed" />
    </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="Overlapping pieces of Intervals" />
      <output name="output" file="gops_intersect_p_diffCols.bed" />
    </test>
    <test>
      <param name="input1" value="1.bed" />
      <param name="input2" value="2.bed" />
      <param name="min" value="10" />
      <param name="returntype" value="Overlapping pieces of Intervals" />
      <output name="output" file="gops_intersect_p_out.bed" />     
    </test>
    <test>
      <param name="input1" value="gops_bigint.interval" ftype="interval" />
      <param name="input2" value="gops_bigint2.interval" ftype="interval" />
      <param name="min" value="1" />
      <param name="returntype" value="" />
      <output name="output" file="gops_intersect_bigint_out.interval" />     
    </test>
    <test>
      <param name="input1" value="gops_bigint2.interval" ftype="interval" />
      <param name="input2" value="gops_bigint.interval" ftype="interval" />
      <param name="min" value="1" />
      <param name="returntype" value="" />
      <output name="output" file="gops_intersect_bigint_out.interval" />     
    </test>
    <test>
      <param name="input1" value="12.bed" ftype="bed" />
      <param name="input2" value="1.bed" ftype="bed" />
      <param name="min" value="1" />
      <param name="returntype" value="" />
      <output name="output" file="gops_intersect_no_strand_out.bed" />     
    </test>
    <!-- Intersect 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_intersect_out2.gff" />        
    </test>
    <!-- Intersect GFF file and bed 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_intersect_out2.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
- **Overlapping Intervals** returns entire intervals from the first dataset  that overlap the second dataset.  The returned intervals are completely unchanged, and this option only filters out intervals that do not overlap with the second dataset.

.. image:: gops_intersectOverlappingIntervals.gif

Overlapping Pieces of Intervals:

.. image:: gops_intersectOverlappingPieces.gif

</help>
</tool>

5:60925436ca5f

<tool id="gops_intersect_1" name="Intersect" 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 '$__tool_directory__/gops_intersect.py'
'$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="returntype" type="select" label="Return" help="(see figure below)">
            <option value="">Overlapping Intervals</option>
            <option value="-p">Overlapping pieces of Intervals</option>
        </param>
        <param name="input1" type="data" format="interval,gff" label="of" help="First dataset" />
        <param name="input2" type="data" format="interval,gff" label="that intersect" help="Second dataset" />
        <param name="min" type="integer" value="1" min="1" label="for at least" 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_intersect_out.bed" />
        </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_intersect_diffCols.bed" />
        </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="Overlapping pieces of Intervals" />
            <output name="output" file="gops_intersect_p_diffCols.bed" />
        </test>
        <test>
            <param name="input1" value="1.bed" />
            <param name="input2" value="2.bed" />
            <param name="min" value="10" />
            <param name="returntype" value="Overlapping pieces of Intervals" />
            <output name="output" file="gops_intersect_p_out.bed" />
        </test>
        <test>
            <param name="input1" value="gops_bigint.interval" ftype="interval" />
            <param name="input2" value="gops_bigint2.interval" ftype="interval" />
            <param name="min" value="1" />
            <param name="returntype" value="" />
            <output name="output" file="gops_intersect_bigint_out.interval" />
        </test>
        <test>
            <param name="input1" value="gops_bigint2.interval" ftype="interval" />
            <param name="input2" value="gops_bigint.interval" ftype="interval" />
            <param name="min" value="1" />
            <param name="returntype" value="" />
            <output name="output" file="gops_intersect_bigint_out.interval" />
        </test>
        <test>
            <param name="input1" value="12.bed" ftype="bed" />
            <param name="input2" value="1.bed" ftype="bed" />
            <param name="min" value="1" />
            <param name="returntype" value="" />
            <output name="output" file="gops_intersect_no_strand_out.bed" />
        </test>
        <!-- Intersect 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_intersect_out2.gff" />
        </test>
        <!-- Intersect GFF file and bed 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_intersect_out2.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
- **Overlapping Intervals** returns entire intervals from the first dataset  that overlap the second dataset.  The returned intervals are completely unchanged, and this option only filters out intervals that do not overlap with the second dataset.

.. image:: gops_intersectOverlappingIntervals.gif

Overlapping Pieces of Intervals:

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