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comparison SMART/galaxy/computeCoverage.xml @ 38:2c0c0a89fad7

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author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
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37:d22fadc825e3 38:2c0c0a89fad7
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