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

Upload GU tool

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GU_files/gu.xml	Fri Jun 15 10:37:45 2012 -0400
@@ -0,0 +1,99 @@
+<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>
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