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comparison SMART/galaxy/GetFlanking.xml @ 36:44d5973c188c

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author m-zytnicki
date Tue, 30 Apr 2013 15:02:29 -0400
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35:d94018ca4ada 36:44d5973c188c
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 </command>
56
57 <inputs>
58 <conditional name="formatType">
59 <param name="FormatInputFileName1" type="select" label="query File Format">
60 <option value="bed">bed</option>
61 <option value="gff">gff</option>
62 <option value="gff2">gff2</option>
63 <option value="gff3">gff3</option>
64 <option value="sam">sam</option>
65 <option value="gtf">gtf</option>
66 </param>
67 <when value="bed">
68 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
69 </when>
70 <when value="gff">
71 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
72 </when>
73 <when value="gff2">
74 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
75 </when>
76 <when value="gff3">
77 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
78 </when>
79 <when value="sam">
80 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
81 </when>
82 <when value="gtf">
83 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
84 </when>
85 </conditional>
86
87 <conditional name="formatType2">
88 <param name="FormatInputFileName2" type="select" label="Refence File Format">
89 <option value="bed">bed</option>
90 <option value="gff">gff</option>
91 <option value="gff2">gff2</option>
92 <option value="gff3">gff3</option>
93 <option value="sam">sam</option>
94 <option value="gtf">gtf</option>
95 </param>
96 <when value="bed">
97 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
98 </when>
99 <when value="gff">
100 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
101 </when>
102 <when value="gff2">
103 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
104 </when>
105 <when value="gff3">
106 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
107 </when>
108 <when value="sam">
109 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
110 </when>
111 <when value="gtf">
112 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
113 </when>
114 </conditional>
115
116 <conditional name="OptionUpDownStream">
117 <param name="OptionUD" type="select" label="Only provide upstream/dowstream features">
118 <option value="UpStream">UpStream</option>
119 <option value="DownStream">DownStream</option>
120 <option value="NONE" selected="true">NONE</option>
121 </param>
122 <when value="UpStream">
123 </when>
124 <when value="DownStream">
125 </when>
126 <when value="NONE">
127 </when>
128 </conditional>
129
130 <conditional name="OptionColinearOrAntiSens">
131 <param name="OptionCA" type="select" label="Only provide collinear/antisens features">
132 <option value="Colinear">Collinear</option>
133 <option value="AntiSens">AntiSens</option>
134 <option value="NONE" selected="true">NONE</option>
135 </param>
136 <when value="Colinear">
137 </when>
138 <when value="AntiSens">
139 </when>
140 <when value="NONE">
141 </when>
142 </conditional>
143
144 <conditional name="OptionMax">
145 <param name="maximum" type="select" label="maximum distance between 2 elements">
146 <option value="Yes">Yes</option>
147 <option value="No" selected="true">No</option>
148 </param>
149 <when value="Yes">
150 <param name="max" type="integer" value="0"/>
151 </when>
152 <when value="No">
153 </when>
154 </conditional>
155
156 <conditional name="OptionMin">
157 <param name="minimum" type="select" label="minimum distance between 2 elements">
158 <option value="Yes">Yes</option>
159 <option value="No" selected="true">No</option>
160 </param>
161 <when value="Yes">
162 <param name="min" type="integer" value="0" />
163 </when>
164 <when value="No">
165 </when>
166 </conditional>
167
168 </inputs>
169
170
171 <outputs>
172 <data format="gff3" name="outputFile" label="[GetFlanking] Output File"/>
173 </outputs>
174
175 <help>
176 This tool prints the elements from the second set of genomic intervals which are closest to (in other words, are flanking) the elements from the first set. You can also play on different parameters:
177
178 - restrict the search to downstream or upstream elements, or print downstream and upstream elements,
179
180 - only consider collinear flanking elements,
181
182 - only consider anti-sense flanking elements,
183
184 - only consider elements which are close enough (using some given distance),
185
186 - only consider flanking elements which do not overlap with the reference element.
187
188 Notice that elements from the second sets may be printed at most once, whether they are the flanking element of several elements from the first or not.
189 </help>
190
191 </tool>