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

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