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

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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="modifyGenomicCoordinates" name="modify genomic coordinates">
2 <description>Extend or shrink a list of genomic coordinates.</description>
3 <command interpreter="python"> ../Java/Python/modifyGenomicCoordinates.py -i $formatType.inputFileName
4 #if $formatType.FormatInputFileName == 'bed':
5 -f bed
6 #elif $formatType.FormatInputFileName == 'gff':
7 -f gff
8 #elif $formatType.FormatInputFileName == 'gff2':
9 -f gff2
10 #elif $formatType.FormatInputFileName == 'gff3':
11 -f gff3
12 #elif $formatType.FormatInputFileName == 'sam':
13 -f sam
14 #elif $formatType.FormatInputFileName == 'gtf':
15 -f gtf
16 #end if
17
18 #if $OptionStart.start == "Yes":
19 -s $OptionStart.startValue
20 #end if
21
22 #if $OptionEnd.end == "Yes":
23 -e $OptionEnd.endValue
24 #end if
25
26 #if $OptionFivePrim.five == "Yes":
27 -5 $OptionFivePrim.fivePValue
28 #end if
29
30 #if $OptionTroisP.TroisP == "Yes":
31 -3 $OptionTroisP.ThreePValue
32 #end if
33
34 -o $outputFile
35 </command>
36
37
38 <inputs>
39 <conditional name="formatType">
40 <param name="FormatInputFileName" type="select" label="Input File Format">
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="inputFileName" format="bed" type="data" label="Input File"/>
50 </when>
51 <when value="gff">
52 <param name="inputFileName" format="gff" type="data" label="Input File"/>
53 </when>
54 <when value="gff2">
55 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
56 </when>
57 <when value="gff3">
58 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
59 </when>
60 <when value="sam">
61 <param name="inputFileName" format="sam" type="data" label="Input File"/>
62 </when>
63 <when value="gtf">
64 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
65 </when>
66 </conditional>
67
68 <conditional name="OptionStart">
69 <param name="start" type="select" label="restrict to the start of the transcript">
70 <option value="Yes">Yes</option>
71 <option value="No" selected="true">No</option>
72 </param>
73 <when value="Yes">
74 <param name="startValue" type="integer" value="0"/>
75 </when>
76 <when value="No">
77 </when>
78 </conditional>
79
80 <conditional name="OptionEnd">
81 <param name="end" type="select" label="restrict to the end of the transcript">
82 <option value="Yes">Yes</option>
83 <option value="No" selected="true">No</option>
84 </param>
85 <when value="Yes">
86 <param name="endValue" type="integer" value="0"/>
87 </when>
88 <when value="No">
89 </when>
90 </conditional>
91
92
93 <conditional name="OptionFivePrim">
94 <param name="five" type="select" label="extend to the 5' direction">
95 <option value="Yes">Yes</option>
96 <option value="No" selected="true">No</option>
97 </param>
98 <when value="Yes">
99 <param name="fivePValue" type="integer" value="0"/>
100 </when>
101 <when value="No">
102 </when>
103 </conditional>
104
105 <conditional name="OptionTroisP">
106 <param name="TroisP" type="select" label="extend to the 3' direction">
107 <option value="Yes">Yes</option>
108 <option value="No" selected="true">No</option>
109 </param>
110 <when value="Yes">
111 <param name="ThreePValue" type="integer" value="0"/>
112 </when>
113 <when value="No">
114 </when>
115 </conditional>
116
117
118 </inputs>
119
120 <outputs>
121 <data format="gff3" name="outputFile" label="[modifyGenomicCoordinates] Output File"/>
122 </outputs>
123
124 <help>
125 </help>
126 </tool>