annotate SMART/galaxy/computeCoverage.xml @ 71:d96f6c9a39e0 draft default tip

Removed pyc files.

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>
00 
01                 <param name="ReportIntron" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Include introns."/>
02 
03         </inputs>
04 
05 	<outputs>
06 		<data name="outputFileGff" format="gff3" label="[compute coverage] output file"/>
07 	</outputs> 
08 	
09 	<help>
10 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.
11 	</help>
12 </tool>
13