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comparison SMART/galaxy/GetFlanking.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="GetFlanking" name="get flanking">
2 <description>Get the flanking regions of a set of reference.</description>
3 <command interpreter="python">
4 ../Java/Python/GetFlanking.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 #if $OptionUpDownStream.OptionUD == 'UpStream':
35 -5
36 #elif $OptionUpDownStream.OptionUD == 'DownStream':
37 -3
38 #end if
39
40
41 #if $OptionColinearOrAntiSens.OptionCA == 'Colinear':
42 -c
43 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
44 -a
45 #end if
46
47 #if $OptionMax.maximum == "Yes":
48 -D $OptionMax.max
49 #end if
50 #if $OptionMin.minimum == "Yes":
51 -d $OptionMin.min
52 #end if
53
54 -o $outputFile
55
56
57
58 </command>
59
60 <inputs>
61 <conditional name="formatType">
62 <param name="FormatInputFileName1" type="select" label="query File Format">
63 <option value="bed">bed</option>
64 <option value="gff">gff</option>
65 <option value="gff2">gff2</option>
66 <option value="gff3">gff3</option>
67 <option value="sam">sam</option>
68 <option value="gtf">gtf</option>
69 </param>
70 <when value="bed">
71 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
72 </when>
73 <when value="gff">
74 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
75 </when>
76 <when value="gff2">
77 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
78 </when>
79 <when value="gff3">
80 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
81 </when>
82 <when value="sam">
83 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
84 </when>
85 <when value="gtf">
86 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
87 </when>
88 </conditional>
89
90 <conditional name="formatType2">
91 <param name="FormatInputFileName2" type="select" label="Refence File Format">
92 <option value="bed">bed</option>
93 <option value="gff">gff</option>
94 <option value="gff2">gff2</option>
95 <option value="gff3">gff3</option>
96 <option value="sam">sam</option>
97 <option value="gtf">gtf</option>
98 </param>
99 <when value="bed">
100 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
101 </when>
102 <when value="gff">
103 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
104 </when>
105 <when value="gff2">
106 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
107 </when>
108 <when value="gff3">
109 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
110 </when>
111 <when value="sam">
112 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
113 </when>
114 <when value="gtf">
115 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
116 </when>
117 </conditional>
118
119 <conditional name="OptionUpDownStream">
120 <param name="OptionUD" type="select" label="UpStream or DownStream">
121 <option value="UpStream">UpStream</option>
122 <option value="DownStream">DownStream</option>
123 <option value="NONE" selected="true">NONE</option>
124 </param>
125 <when value="UpStream">
126 </when>
127 <when value="DownStream">
128 </when>
129 <when value="NONE">
130 </when>
131 </conditional>
132
133 <conditional name="OptionColinearOrAntiSens">
134 <param name="OptionCA" type="select" label="Colinear or anti-sens">
135 <option value="Colinear">Colinear</option>
136 <option value="AntiSens">AntiSens</option>
137 <option value="NONE" selected="true">NONE</option>
138 </param>
139 <when value="Colinear">
140 </when>
141 <when value="AntiSens">
142 </when>
143 <when value="NONE">
144 </when>
145 </conditional>
146
147 <conditional name="OptionMax">
148 <param name="maximum" type="select" label="maximum distance between 2 elements">
149 <option value="Yes">Yes</option>
150 <option value="No" selected="true">No</option>
151 </param>
152 <when value="Yes">
153 <param name="max" type="integer" value="0"/>
154 </when>
155 <when value="No">
156 </when>
157 </conditional>
158
159 <conditional name="OptionMin">
160 <param name="minimum" type="select" label="minimum distance between 2 elements">
161 <option value="Yes">Yes</option>
162 <option value="No" selected="true">No</option>
163 </param>
164 <when value="Yes">
165 <param name="min" type="integer" value="0" />
166 </when>
167 <when value="No">
168 </when>
169 </conditional>
170
171 </inputs>
172
173
174 <outputs>
175 <data format="gff3" name="outputFile" label="[GetFlanking] Output File"/>
176 </outputs>
177
178
179 </tool>