view GU_files/gu.xml @ 0:a792b0548fe9 draft default tip

Upload GU tool

<tool id="gu" name="GU" version="0.0.1">
  <description>Comparing genomic information overlap between two files</description>
  <command interpreter="python">
    GU.py
        --f1 $input1
  		--f2 $input2
  		--minOverlap $minOverlap
  		--ignoreStrand $ignoreStrand
  		--noSelfHits $noSelfHits
  		--chrMatchLoose $chrMatching
  		--noAggregate $noAggregate
  		$selectType1
  		$selectType2
  		$NotSelectType1
  		$NotSelectType2
  		-l LOG
  </command>
  <inputs>
    <param format="tabular" name="input1" type="data" label="First Data File"/>
    <param format="tabular" name="input2" type="data" label="Second Data File"/>
  	<param name="minOverlap" type="text" size="5" value="1" label="Minimum Overlap" help="The minimum coordinate required overlap."/>
	<param name="noSelfHits" type="select" label="Ignore Self Hits in Overlap Detection" help="Ignore self-hit in overlap detection. (default: reports self-hits)">
		<option value="False">False</option>
		<option value="True">True</option>
    </param>
  	<param name="ignoreStrand" type="select" label="Ignore Strand" help="Ignore strand when determining overlaps (Default = strands must match).">
  		<option value="False">No</option>
		<option value="True">Yes</option>
    </param>
	<param name="noSelfHits" type="select" label="Ignore Self Hits in Overlap Detection" help="If specified, chromosome matching is 'loose'. Otherwise it is exact. In loose matching, leading 'chr' is removed from chromosome field, so that '19' matches 'Chr19'.">
		<option value="False">Off</option>
		<option value="True">On</option>
    </param>
	<param name="chrMatching" type="select" label="Loose Chromosome Matching">
		<option value="False">Off</option>
		<option value="True">On</option>
    </param>
    <param name="noAggregate" type="select" label="Aggregate Mode" help="Default is non-aggregate mode.">
    	<option value="False">Off</option>
    	<option value="True">On</option>
    </param>
    <param name="selectType1" type="select" label="Select First Feature to Include" multiple="True" help="A GFF type to select from file 1.">
  		<option value="">All</option>
  		<option value="--t1 Exon">Exon</option>
  		<option value="--t1 Gene">Gene</option>
  		<option value="--t1 Pseudogene">Pseudogene</option>
  		<option value="--t1 QTL">QTL</option>
    </param>
    <param name="selectType2" type="select" label="Select Second Feature to Include" multiple="True" help="A GFF type to select from file 2.">
  		<option value="">All</option>
  		<option value="--t1 Exon">Exon</option>
  		<option value="--t1 Gene">Gene</option>
  		<option value="--t1 Pseudogene">Pseudogene</option>
  		<option value="--t1 QTL">QTL</option>
    </param>
    <param name="NotSelectType1" type="select" label="Select First Feature to Exclude" multiple="True" help="A GFF type to select from file 1.">
  		<option value="">All</option>
  		<option value="--t1 Exon">Exon</option>
  		<option value="--t1 Gene">Gene</option>
  		<option value="--t1 Pseudogene">Pseudogene</option>
  		<option value="--t1 QTL">QTL</option>
    </param>
    <param name="NotSelectType2" type="select" label="Select Second Feature to Exclude" multiple="True" help="A GFF type to select from file 2.">
  		<option value="">All</option>
  		<option value="--t1 Exon">Exon</option>
  		<option value="--t1 Gene">Gene</option>
  		<option value="--t1 Pseudogene">Pseudogene</option>
  		<option value="--t1 QTL">QTL</option>
    </param>        
  </inputs>
  <help>
.. class:: warningmark

Aggregate mode does not work in this build.

**Function**

Finds overlap between two data sets, narrowed by given parameter.

This tool is still in deveopment.

  </help>
  <outputs>
    <data format="tabular" name="output1" label="0-1 Bucket" from_work_dir="bucket_0-1.txt" />
    <data format="tabular" name="output2" label="1-0 Bucket" from_work_dir="bucket_1-0.txt" />
    <data format="tabular" name="output3" label="1-1 Bucket" from_work_dir="bucket_1-1.txt" />
    <data format="tabular" name="output4" label="1-n Bucket" from_work_dir="bucket_1-n.txt" />
    <data format="tabular" name="output5" label="n-1 Bucket" from_work_dir="bucket_n-1.txt" />
  	<data format="tabular" name="output6" label="n-m Bucket" from_work_dir="bucket_n-m.txt" />
  </outputs>

  <tests>
    <test>
      <param name="input" value="fa_gc_content_input.fa"/>
      <output name="out_file1" file="fa_gc_content_output.txt"/>
    </test>
  </tests>

</tool>