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comparison TEiso/ClosestToStartSite_Wrapper.xml @ 0:3d22562b4489 draft

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author urgi-team
date Fri, 29 Apr 2016 09:11:18 -0400
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children 15d6811e6bf5
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1 <tool id="ClosestToStartSite" name="ClosestToStartSite" version="1.0">
2 <description>ClosestToStartSite parses a bed file and create a bed file to create a report about positions of features A to features B.</description>
3 <requirements>
4 <requirement type="package" version="1.0">TEiso_Tools</requirement>
5 </requirements>
6 <version_command>
7 ClosestToStartSite.py --version
8 </version_command>
9 <command interpreter="python">
10 ClosestToStartSite_Wrapper.py -i $inputFile -o $outputFile
11 </command>
12 <inputs>
13 <param name="inputFile" type="data" format="bed" label="indicate a bed file."/>
14 </inputs>
15 <outputs>
16 <data name="outputFile" format="bed" label="${tool.name} on ${on_string} (BED)"/>
17 </outputs>
18 <help><![CDATA[
19
20 **ClosestToStartSite_wrapper parses a bed file and create a bed file to create a report about positions of features A to features B.**
21
22
23 **what it does :**
24
25 parses a bed file and create a bed file to create a report about positions of features A to features B
26
27 -----
28
29 **input format :**
30
31 .. class:: infomark
32
33 **output format :**
34
35 fake 140 532 CUFF.1.1 CUFF.1 + 26875.607
36
37 -----
38
39
40
41 ****** "B_close_TSS"
42 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
43
44 F[1] gene F[2]
45 =========================>
46 ------------
47 F[8] F[9]
48
49
50 F[1] F[2]
51 <=========================
52 ---------------
53
54
55 ****** "B_overlap_TSS"
56 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
57
58 F[1] gene F[2]
59 =========================>
60 -------------
61 F[8] F[9]
62
63 gene
64 F[1]=========================>F[2]
65
66 F[8]---------------F[9]
67
68
69
70 F[1]=============================>F[2]
71 F[8]---------------F[9]
72
73
74 F[1]<=============================F[2]
75 ---------------------------
76 F[8] F[9]
77
78
79 F[1]<=============================F[2]
80 F[8]---------------F[9]
81
82
83 F[1]<=============================F[2]
84 F[8]---------------F[9]
85
86 ****** "B-inclus-A"
87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
88
89
90
91 F[1] gene F[2]
92 ==============================
93 -------------
94 F[8] F[9]
95
96 ****** "A-inclus-B"
97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
98
99
100 F[1]======================F[2]
101 F[8]----------------------------------------------------F[9]
102
103
104
105
106 F[1]==================================>F[2]
107 F[8]----------------------------------------------------------F[9]
108
109
110
111 F[1]<==================================F[2]
112 F[8]----------------------------------------------------------F[9]
113
114
115
116 ****** "A-inclus-B-inTSS"
117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
118
119 F[1]<==================================F[2]
120 [8]----------------------------------------------------------F[9]
121
122
123 F[1]==================================>F[2]
124 F[8]----------------------------------------------------------F[9]
125
126
127 -----
128
129 **reference :**
130
131 ]]>
132 </help>
133 </tool>