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comparison SMART/galaxy/mergeSlidingWindowsClusters.xml @ 6:769e306b7933

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Change the repository level.
author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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children 440ceca58672
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5:ea3082881bf8 6:769e306b7933
1 <tool id="mergeSlidingWindowsClusters" name="merge sliding windows clusters">
2 <description>Merges two files containing the results of a sliding windows clustering.</description>
3 <command interpreter="python">
4 ../Java/Python/mergeSlidingWindowsClusters.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 -o $outputFileGff
35
36 </command>
37
38 <inputs>
39 <conditional name="formatType">
40 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
41 <option value="bed">bed</option>
42 <option value="gff">gff</option>
43 <option value="gff2">gff2</option>
44 <option value="gff3">gff3</option>
45 <option value="sam">sam</option>
46 <option value="gtf">gtf</option>
47 </param>
48 <when value="bed">
49 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
50 </when>
51 <when value="gff">
52 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
53 </when>
54 <when value="gff2">
55 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
56 </when>
57 <when value="gff3">
58 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
59 </when>
60 <when value="sam">
61 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
62 </when>
63 <when value="gtf">
64 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
65 </when>
66 </conditional>
67
68 <conditional name="formatType2">
69 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
70 <option value="bed">bed</option>
71 <option value="gff">gff</option>
72 <option value="gff2">gff2</option>
73 <option value="gff3">gff3</option>
74 <option value="sam">sam</option>
75 <option value="gtf">gtf</option>
76 </param>
77 <when value="bed">
78 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
79 </when>
80 <when value="gff">
81 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
82 </when>
83 <when value="gff2">
84 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
85 </when>
86 <when value="gff3">
87 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
88 </when>
89 <when value="sam">
90 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
91 </when>
92 <when value="gtf">
93 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
94 </when>
95 </conditional>
96
97 </inputs>
98
99 <outputs>
100 <data name="outputFileGff" format="gff3"/>
101 </outputs>
102
103 </tool>