|
38
|
1 <tool id="ComputeCoverage" name="compute coverage">
|
|
|
2 <description>Compute the coverage of a set with respect to another set.</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="set_environment">PYTHONPATH</requirement>
|
|
|
5 </requirements>
|
|
|
6 <command interpreter="python">
|
|
|
7 ../Java/Python/ComputeCoverage.py -i $formatType.inputFileName1
|
|
|
8 #if $formatType.FormatInputFileName1 == 'bed':
|
|
|
9 -f bed
|
|
|
10 #elif $formatType.FormatInputFileName1 == 'gff':
|
|
|
11 -f gff
|
|
|
12 #elif $formatType.FormatInputFileName1 == 'gff2':
|
|
|
13 -f gff2
|
|
|
14 #elif $formatType.FormatInputFileName1 == 'gff3':
|
|
|
15 -f gff3
|
|
|
16 #elif $formatType.FormatInputFileName1 == 'sam':
|
|
|
17 -f sam
|
|
|
18 #elif $formatType.FormatInputFileName1 == 'gtf':
|
|
|
19 -f gtf
|
|
|
20 #end if
|
|
|
21
|
|
|
22 -j $formatType2.inputFileName2
|
|
|
23 #if $formatType2.FormatInputFileName2 == 'bed':
|
|
|
24 -g bed
|
|
|
25 #elif $formatType2.FormatInputFileName2 == 'gff':
|
|
|
26 -g gff
|
|
|
27 #elif $formatType2.FormatInputFileName2 == 'gff2':
|
|
|
28 -g gff2
|
|
|
29 #elif $formatType2.FormatInputFileName2 == 'gff3':
|
|
|
30 -g gff3
|
|
|
31 #elif $formatType2.FormatInputFileName2 == 'sam':
|
|
|
32 -g sam
|
|
|
33 #elif $formatType2.FormatInputFileName2 == 'gtf':
|
|
|
34 -g gtf
|
|
|
35 #end if
|
|
|
36
|
|
|
37 $ReportIntron
|
|
|
38 -o $outputFileGff
|
|
|
39
|
|
|
40 </command>
|
|
|
41
|
|
|
42 <inputs>
|
|
|
43 <conditional name="formatType">
|
|
|
44 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
|
|
|
45 <option value="bed">bed</option>
|
|
|
46 <option value="gff">gff</option>
|
|
|
47 <option value="gff2">gff2</option>
|
|
|
48 <option value="gff3">gff3</option>
|
|
|
49 <option value="sam">sam</option>
|
|
|
50 <option value="gtf">gtf</option>
|
|
|
51 </param>
|
|
|
52 <when value="bed">
|
|
|
53 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
|
|
|
54 </when>
|
|
|
55 <when value="gff">
|
|
|
56 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
|
|
|
57 </when>
|
|
|
58 <when value="gff2">
|
|
|
59 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
|
|
|
60 </when>
|
|
|
61 <when value="gff3">
|
|
|
62 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
|
|
|
63 </when>
|
|
|
64 <when value="sam">
|
|
|
65 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
|
|
|
66 </when>
|
|
|
67 <when value="gtf">
|
|
|
68 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
|
|
|
69 </when>
|
|
|
70 </conditional>
|
|
|
71
|
|
|
72 <conditional name="formatType2">
|
|
|
73 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
|
|
|
74 <option value="bed">bed</option>
|
|
|
75 <option value="gff">gff</option>
|
|
|
76 <option value="gff2">gff2</option>
|
|
|
77 <option value="gff3">gff3</option>
|
|
|
78 <option value="sam">sam</option>
|
|
|
79 <option value="gtf">gtf</option>
|
|
|
80 </param>
|
|
|
81 <when value="bed">
|
|
|
82 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
|
|
|
83 </when>
|
|
|
84 <when value="gff">
|
|
|
85 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
|
|
|
86 </when>
|
|
|
87 <when value="gff2">
|
|
|
88 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
|
|
|
89 </when>
|
|
|
90 <when value="gff3">
|
|
|
91 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
|
|
|
92 </when>
|
|
|
93 <when value="sam">
|
|
|
94 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
|
|
|
95 </when>
|
|
|
96 <when value="gtf">
|
|
|
97 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
|
|
|
98 </when>
|
|
|
99 </conditional>
|
|
|
100
|
|
|
101 <param name="ReportIntron" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Include introns."/>
|
|
|
102
|
|
|
103 </inputs>
|
|
|
104
|
|
|
105 <outputs>
|
|
|
106 <data name="outputFileGff" format="gff3" label="[compute coverage] output file"/>
|
|
|
107 </outputs>
|
|
|
108
|
|
|
109 <help>
|
|
|
110 This tool considers a query and a reference files, and gives the coverage of the query file by the reference. The output file is similar to the query file, where a tag **coverage** has been added.
|
|
|
111 </help>
|
|
|
112 </tool>
|
|
|
113
|
