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comparison TEiso/ClosestToStartSite_Wrapper.xml @ 1:15d6811e6bf5 draft

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author urgi-team
date Tue, 24 May 2016 08:59:28 -0400
parents 3d22562b4489
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0:3d22562b4489 1:15d6811e6bf5
1 <tool id="ClosestToStartSite" name="ClosestToStartSite" version="1.0"> 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> 2 <description>ClosestToStartSite parses a bed file and generate a report about positions of features A to features B. It can also add the class code of features A.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0">TEiso_Tools</requirement> 4 <requirement type="package" version="1.0">TEiso_Tools</requirement>
5 </requirements> 5 </requirements>
6 <version_command> 6 <version_command>
7 ClosestToStartSite.py --version 7 ClosestToStartSite.py --version
8 </version_command> 8 </version_command>
9 <command interpreter="python"> 9 <command interpreter="python">
10 ClosestToStartSite_Wrapper.py -i $inputFile -o $outputFile 10 #if $ClassCode.get_class_code
11 ClosestToStartSite_Wrapper.py -i $inputFile -c $cuffcom_tmap -o $outputFile
12 #else
13 ClosestToStartSite_Wrapper.py -i $inputFile -o $outputFile
14 #end if
11 </command> 15 </command>
12 <inputs> 16 <inputs>
13 <param name="inputFile" type="data" format="bed" label="indicate a bed file."/> 17 <param name="inputFile" type="data" format="bed" label="indicate a bed file."/>
18 <conditional name="ClassCode">
19 <param name="get_class_code" type="boolean" label="get information of class code from cuff_in.tmap" truevalue="yes" falsevalue="no" checked="off" />
20 <when value="no"/>
21 <when value="yes">
22 <param name="cuffcom_tmap" type="data" format="tabular" label="indicate cuff_in.tmap" help="default = 1"/>
23 </when>
24 </conditional>
14 </inputs> 25 </inputs>
15 <outputs> 26 <outputs>
16 <data name="outputFile" format="bed" label="${tool.name} on ${on_string} (BED)"/> 27 <data name="outputFile" format="bed" label="${tool.name} on ${on_string} (BED)"/>
17 </outputs> 28 </outputs>
18 <help><![CDATA[ 29 <help><![CDATA[
19 30
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 31
32
33
34 **ClosestToStartSite parses a bed file and generate a report about positions of features A (according to its TSS) to features B. It can also add the class code of features A.**
22 35
23 **what it does :** 36 **what it does :**
24 37
25 parses a bed file and create a bed file to create a report about positions of features A to features B 38 generate a report about positions of features B to features A (according to its TSS). In input file, there are the information of the two features. ClosestToStartSite reports only the cases that features Bis near to TSS or has overlap with TSS of features A. it can be also run cuffcopare to features A, and add the class code information to output file.
39
26 40
27 ----- 41 -----
28 42
29 **input format :** 43 **example :**
30
31 .. class:: infomark
32
33 **output format :**
34
35 fake 140 532 CUFF.1.1 CUFF.1 + 26875.607
36
37 -----
38 44
39 45
46 Bed input file: ::
40 47
41 ****** "B_close_TSS" 48 2L 239751 240346 CUFF.36.1 CUFF.36 - 2L 239932 241306 RXX + 415 TE_overlap_TSS
42 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 49 2L 113233 113411 CUFF.14.1 CUFF.14 - 2L 113496 113509 RLX - -854 TE_near_TSS
43
44 F[1] gene F[2]
45 =========================>
46 ------------
47 F[8] F[9]
48
49
50 F[1] F[2]
51 <=========================
52 ---------------
53 50
54 51
55 ****** "B_overlap_TSS" 52 ----
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 53
86 ****** "B-inclus-A" 54 output format: ::
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 55
129 **reference :** 56
57 2L 239751 240346 CUFF.36.1 CUFF.36 - 2L 239932 241306 RXX + 415 TE_overlap_TSS
58 2L 113233 113411 CUFF.14.1 CUFF.14 - 2L 113496 113509 RLX - -854 TE_near_TSS
59
60
61 output format with calss code: ::
62
63
64 2L 239751 240346 CUFF.36.1 CUFF.36 - 2L 239932 241306 RXX + 415 TE_overlap_TSS c gene-id-1
65 2L 113233 113411 CUFF.14.1 CUFF.14 - 2L 113496 113509 RLX - -854 TE_near_TSS = gene-id-2
66
130 67
131 ]]> 68 ]]>
132 </help> 69 </help>
133 </tool> 70 </tool>