|
0
|
1 <tool id="gu" name="GU" version="0.0.1">
|
|
|
2 <description>Comparing genomic information overlap between two files</description>
|
|
|
3 <command interpreter="python">
|
|
|
4 GU.py
|
|
|
5 --f1 $input1
|
|
|
6 --f2 $input2
|
|
|
7 --minOverlap $minOverlap
|
|
|
8 --ignoreStrand $ignoreStrand
|
|
|
9 --noSelfHits $noSelfHits
|
|
|
10 --chrMatchLoose $chrMatching
|
|
|
11 --noAggregate $noAggregate
|
|
|
12 $selectType1
|
|
|
13 $selectType2
|
|
|
14 $NotSelectType1
|
|
|
15 $NotSelectType2
|
|
|
16 -l LOG
|
|
|
17 </command>
|
|
|
18 <inputs>
|
|
|
19 <param format="tabular" name="input1" type="data" label="First Data File"/>
|
|
|
20 <param format="tabular" name="input2" type="data" label="Second Data File"/>
|
|
|
21 <param name="minOverlap" type="text" size="5" value="1" label="Minimum Overlap" help="The minimum coordinate required overlap."/>
|
|
|
22 <param name="noSelfHits" type="select" label="Ignore Self Hits in Overlap Detection" help="Ignore self-hit in overlap detection. (default: reports self-hits)">
|
|
|
23 <option value="False">False</option>
|
|
|
24 <option value="True">True</option>
|
|
|
25 </param>
|
|
|
26 <param name="ignoreStrand" type="select" label="Ignore Strand" help="Ignore strand when determining overlaps (Default = strands must match).">
|
|
|
27 <option value="False">No</option>
|
|
|
28 <option value="True">Yes</option>
|
|
|
29 </param>
|
|
|
30 <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'.">
|
|
|
31 <option value="False">Off</option>
|
|
|
32 <option value="True">On</option>
|
|
|
33 </param>
|
|
|
34 <param name="chrMatching" type="select" label="Loose Chromosome Matching">
|
|
|
35 <option value="False">Off</option>
|
|
|
36 <option value="True">On</option>
|
|
|
37 </param>
|
|
|
38 <param name="noAggregate" type="select" label="Aggregate Mode" help="Default is non-aggregate mode.">
|
|
|
39 <option value="False">Off</option>
|
|
|
40 <option value="True">On</option>
|
|
|
41 </param>
|
|
|
42 <param name="selectType1" type="select" label="Select First Feature to Include" multiple="True" help="A GFF type to select from file 1.">
|
|
|
43 <option value="">All</option>
|
|
|
44 <option value="--t1 Exon">Exon</option>
|
|
|
45 <option value="--t1 Gene">Gene</option>
|
|
|
46 <option value="--t1 Pseudogene">Pseudogene</option>
|
|
|
47 <option value="--t1 QTL">QTL</option>
|
|
|
48 </param>
|
|
|
49 <param name="selectType2" type="select" label="Select Second Feature to Include" multiple="True" help="A GFF type to select from file 2.">
|
|
|
50 <option value="">All</option>
|
|
|
51 <option value="--t1 Exon">Exon</option>
|
|
|
52 <option value="--t1 Gene">Gene</option>
|
|
|
53 <option value="--t1 Pseudogene">Pseudogene</option>
|
|
|
54 <option value="--t1 QTL">QTL</option>
|
|
|
55 </param>
|
|
|
56 <param name="NotSelectType1" type="select" label="Select First Feature to Exclude" multiple="True" help="A GFF type to select from file 1.">
|
|
|
57 <option value="">All</option>
|
|
|
58 <option value="--t1 Exon">Exon</option>
|
|
|
59 <option value="--t1 Gene">Gene</option>
|
|
|
60 <option value="--t1 Pseudogene">Pseudogene</option>
|
|
|
61 <option value="--t1 QTL">QTL</option>
|
|
|
62 </param>
|
|
|
63 <param name="NotSelectType2" type="select" label="Select Second Feature to Exclude" multiple="True" help="A GFF type to select from file 2.">
|
|
|
64 <option value="">All</option>
|
|
|
65 <option value="--t1 Exon">Exon</option>
|
|
|
66 <option value="--t1 Gene">Gene</option>
|
|
|
67 <option value="--t1 Pseudogene">Pseudogene</option>
|
|
|
68 <option value="--t1 QTL">QTL</option>
|
|
|
69 </param>
|
|
|
70 </inputs>
|
|
|
71 <help>
|
|
|
72 .. class:: warningmark
|
|
|
73
|
|
|
74 Aggregate mode does not work in this build.
|
|
|
75
|
|
|
76 **Function**
|
|
|
77
|
|
|
78 Finds overlap between two data sets, narrowed by given parameter.
|
|
|
79
|
|
|
80 This tool is still in deveopment.
|
|
|
81
|
|
|
82 </help>
|
|
|
83 <outputs>
|
|
|
84 <data format="tabular" name="output1" label="0-1 Bucket" from_work_dir="bucket_0-1.txt" />
|
|
|
85 <data format="tabular" name="output2" label="1-0 Bucket" from_work_dir="bucket_1-0.txt" />
|
|
|
86 <data format="tabular" name="output3" label="1-1 Bucket" from_work_dir="bucket_1-1.txt" />
|
|
|
87 <data format="tabular" name="output4" label="1-n Bucket" from_work_dir="bucket_1-n.txt" />
|
|
|
88 <data format="tabular" name="output5" label="n-1 Bucket" from_work_dir="bucket_n-1.txt" />
|
|
|
89 <data format="tabular" name="output6" label="n-m Bucket" from_work_dir="bucket_n-m.txt" />
|
|
|
90 </outputs>
|
|
|
91
|
|
|
92 <tests>
|
|
|
93 <test>
|
|
|
94 <param name="input" value="fa_gc_content_input.fa"/>
|
|
|
95 <output name="out_file1" file="fa_gc_content_output.txt"/>
|
|
|
96 </test>
|
|
|
97 </tests>
|
|
|
98
|
|
|
99 </tool> |
