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comparison SMART/galaxy/computeCoverage.xml @ 36:44d5973c188c

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author m-zytnicki
date Tue, 30 Apr 2013 15:02:29 -0400
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35:d94018ca4ada 36:44d5973c188c
1 <tool id="ComputeCoverage" name="compute coverage">
2 <description>Compute the coverage of a set with respect to another set.</description>
3 <command interpreter="python">
4 ../Java/Python/ComputeCoverage.py -i $formatType.inputFileName1
5 #if $formatType.FormatInputFileName1 == 'bed':
6 -f bed
7 #elif $formatType.FormatInputFileName1 == 'gff':
8 -f gff
9 #elif $formatType.FormatInputFileName1 == 'gff2':
10 -f gff2
11 #elif $formatType.FormatInputFileName1 == 'gff3':
12 -f gff3
13 #elif $formatType.FormatInputFileName1 == 'sam':
14 -f sam
15 #elif $formatType.FormatInputFileName1 == 'gtf':
16 -f gtf
17 #end if
18
19 -j $formatType2.inputFileName2
20 #if $formatType2.FormatInputFileName2 == 'bed':
21 -g bed
22 #elif $formatType2.FormatInputFileName2 == 'gff':
23 -g gff
24 #elif $formatType2.FormatInputFileName2 == 'gff2':
25 -g gff2
26 #elif $formatType2.FormatInputFileName2 == 'gff3':
27 -g gff3
28 #elif $formatType2.FormatInputFileName2 == 'sam':
29 -g sam
30 #elif $formatType2.FormatInputFileName2 == 'gtf':
31 -g gtf
32 #end if
33
34 $ReportIntron
35 -o $outputFileGff
36
37 </command>
38
39 <inputs>
40 <conditional name="formatType">
41 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
42 <option value="bed">bed</option>
43 <option value="gff">gff</option>
44 <option value="gff2">gff2</option>
45 <option value="gff3">gff3</option>
46 <option value="sam">sam</option>
47 <option value="gtf">gtf</option>
48 </param>
49 <when value="bed">
50 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
51 </when>
52 <when value="gff">
53 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
54 </when>
55 <when value="gff2">
56 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
57 </when>
58 <when value="gff3">
59 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
60 </when>
61 <when value="sam">
62 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
63 </when>
64 <when value="gtf">
65 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
66 </when>
67 </conditional>
68
69 <conditional name="formatType2">
70 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
71 <option value="bed">bed</option>
72 <option value="gff">gff</option>
73 <option value="gff2">gff2</option>
74 <option value="gff3">gff3</option>
75 <option value="sam">sam</option>
76 <option value="gtf">gtf</option>
77 </param>
78 <when value="bed">
79 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
80 </when>
81 <when value="gff">
82 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
83 </when>
84 <when value="gff2">
85 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
86 </when>
87 <when value="gff3">
88 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
89 </when>
90 <when value="sam">
91 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
92 </when>
93 <when value="gtf">
94 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
95 </when>
96 </conditional>
97
98 <param name="ReportIntron" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Include introns."/>
99
100 </inputs>
101
102 <outputs>
103 <data name="outputFileGff" format="gff3" label="[computeCoverage] OUTPUT file"/>
104 </outputs>
105
106 <help>
107 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.
108 </help>
109 </tool>
110