Mercurial > repos > yufei-luo > s_mart

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 15:02:29 -0400
parents
children
comparison
equal deleted inserted replaced
35:d94018ca4ada 36:44d5973c188c
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 <help>
104 Sliding windows are also useful to compare two (or more!) sets of data. This can be very valuable when you want to compare differential expression in two different conditions. When you have two different sliding windows sets, this function merges them into one, where each window contains the two pieces of information. You may want to plot the data afterwards using the *plot transcript list* function.
105 </help>
106
107 </tool>