|
6
|
1 <tool id="modifyGenomicCoordinates" name="modify genomic coordinates">
|
|
|
2 <description>Extend or shrink a list of genomic coordinates.</description>
|
|
18
|
3 <requirements>
|
|
|
4 <requirement type="set_environment">PYTHONPATH</requirement>
|
|
|
5 </requirements>
|
|
6
|
6 <command interpreter="python"> ../Java/Python/modifyGenomicCoordinates.py -i $formatType.inputFileName
|
|
|
7 #if $formatType.FormatInputFileName == 'bed':
|
|
|
8 -f bed
|
|
|
9 #elif $formatType.FormatInputFileName == 'gff':
|
|
|
10 -f gff
|
|
|
11 #elif $formatType.FormatInputFileName == 'gff2':
|
|
|
12 -f gff2
|
|
|
13 #elif $formatType.FormatInputFileName == 'gff3':
|
|
|
14 -f gff3
|
|
|
15 #elif $formatType.FormatInputFileName == 'sam':
|
|
|
16 -f sam
|
|
|
17 #elif $formatType.FormatInputFileName == 'gtf':
|
|
|
18 -f gtf
|
|
|
19 #end if
|
|
|
20
|
|
|
21 #if $OptionStart.start == "Yes":
|
|
|
22 -s $OptionStart.startValue
|
|
|
23 #end if
|
|
|
24
|
|
|
25 #if $OptionEnd.end == "Yes":
|
|
|
26 -e $OptionEnd.endValue
|
|
|
27 #end if
|
|
|
28
|
|
|
29 #if $OptionFivePrim.five == "Yes":
|
|
|
30 -5 $OptionFivePrim.fivePValue
|
|
|
31 #end if
|
|
|
32
|
|
|
33 #if $OptionTroisP.TroisP == "Yes":
|
|
|
34 -3 $OptionTroisP.ThreePValue
|
|
|
35 #end if
|
|
|
36
|
|
|
37 -o $outputFile
|
|
|
38 </command>
|
|
|
39
|
|
|
40
|
|
|
41 <inputs>
|
|
|
42 <conditional name="formatType">
|
|
|
43 <param name="FormatInputFileName" type="select" label="Input File Format">
|
|
|
44 <option value="bed">bed</option>
|
|
|
45 <option value="gff">gff</option>
|
|
|
46 <option value="gff2">gff2</option>
|
|
|
47 <option value="gff3">gff3</option>
|
|
|
48 <option value="sam">sam</option>
|
|
|
49 <option value="gtf">gtf</option>
|
|
|
50 </param>
|
|
|
51 <when value="bed">
|
|
|
52 <param name="inputFileName" format="bed" type="data" label="Input File"/>
|
|
|
53 </when>
|
|
|
54 <when value="gff">
|
|
|
55 <param name="inputFileName" format="gff" type="data" label="Input File"/>
|
|
|
56 </when>
|
|
|
57 <when value="gff2">
|
|
|
58 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
|
|
|
59 </when>
|
|
|
60 <when value="gff3">
|
|
|
61 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
|
|
|
62 </when>
|
|
|
63 <when value="sam">
|
|
|
64 <param name="inputFileName" format="sam" type="data" label="Input File"/>
|
|
|
65 </when>
|
|
|
66 <when value="gtf">
|
|
|
67 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
|
|
|
68 </when>
|
|
|
69 </conditional>
|
|
|
70
|
|
|
71 <conditional name="OptionStart">
|
|
15
|
72 <param name="start" type="select" label="shrink to the start of the feature">
|
|
6
|
73 <option value="Yes">Yes</option>
|
|
|
74 <option value="No" selected="true">No</option>
|
|
|
75 </param>
|
|
|
76 <when value="Yes">
|
|
|
77 <param name="startValue" type="integer" value="0"/>
|
|
|
78 </when>
|
|
|
79 <when value="No">
|
|
|
80 </when>
|
|
|
81 </conditional>
|
|
|
82
|
|
|
83 <conditional name="OptionEnd">
|
|
15
|
84 <param name="end" type="select" label="shrink to the end of the feature">
|
|
6
|
85 <option value="Yes">Yes</option>
|
|
|
86 <option value="No" selected="true">No</option>
|
|
|
87 </param>
|
|
|
88 <when value="Yes">
|
|
|
89 <param name="endValue" type="integer" value="0"/>
|
|
|
90 </when>
|
|
|
91 <when value="No">
|
|
|
92 </when>
|
|
|
93 </conditional>
|
|
|
94
|
|
|
95
|
|
|
96 <conditional name="OptionFivePrim">
|
|
|
97 <param name="five" type="select" label="extend to the 5' direction">
|
|
|
98 <option value="Yes">Yes</option>
|
|
|
99 <option value="No" selected="true">No</option>
|
|
|
100 </param>
|
|
|
101 <when value="Yes">
|
|
|
102 <param name="fivePValue" type="integer" value="0"/>
|
|
|
103 </when>
|
|
|
104 <when value="No">
|
|
|
105 </when>
|
|
|
106 </conditional>
|
|
|
107
|
|
|
108 <conditional name="OptionTroisP">
|
|
|
109 <param name="TroisP" type="select" label="extend to the 3' direction">
|
|
|
110 <option value="Yes">Yes</option>
|
|
|
111 <option value="No" selected="true">No</option>
|
|
|
112 </param>
|
|
|
113 <when value="Yes">
|
|
|
114 <param name="ThreePValue" type="integer" value="0"/>
|
|
|
115 </when>
|
|
|
116 <when value="No">
|
|
|
117 </when>
|
|
|
118 </conditional>
|
|
|
119
|
|
|
120
|
|
|
121 </inputs>
|
|
|
122
|
|
|
123 <outputs>
|
|
18
|
124 <data format="gff3" name="outputFile" label="[modify genomic coordinates] output file"/>
|
|
6
|
125 </outputs>
|
|
|
126
|
|
|
127 <help>
|
|
15
|
128 This tool reads a list of transcripts and modifies each feature by:
|
|
|
129
|
|
18
|
130 - shrinking it to the *n* first nucleotides or the *n* last nucleotides, or
|
|
15
|
131
|
|
18
|
132 - extending it to *n* nucleotides towards the 5' direction (upstream) or the 3' direction (downstream).
|
|
15
|
133
|
|
|
134 Note that the 5' or 3' direction depends on the orientation of the feature (the 5' end of a transcript located on the minus strand is on the right hand of this transcript!).
|
|
|
135
|
|
|
136 The tool needs a transcript file, its format, and outputs a new transcript file.
|
|
6
|
137 </help>
|
|
|
138 </tool>
|
