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comparison SMART/galaxy/GetFlanking.xml @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
1 <tool id="GetFlanking" name="get flanking"> 1 <tool id="GetFlanking" name="get flanking">
2 <description>Get the flanking regions of a set of reference.</description> 2 <description>Get the flanking regions of a set of reference.</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python"> 3 <command interpreter="python">
7 ../Java/Python/GetFlanking.py -i $formatType.inputFileName1 4 ../Java/Python/GetFlanking.py -i $formatType.inputFileName1
8 #if $formatType.FormatInputFileName1 == 'bed': 5 #if $formatType.FormatInputFileName1 == 'bed':
9 -f bed 6 -f bed
10 #elif $formatType.FormatInputFileName1 == 'gff': 7 #elif $formatType.FormatInputFileName1 == 'gff':
53 #if $OptionMin.minimum == "Yes": 50 #if $OptionMin.minimum == "Yes":
54 -d $OptionMin.min 51 -d $OptionMin.min
55 #end if 52 #end if
56 53
57 -o $outputFile 54 -o $outputFile
55
56
57
58 </command> 58 </command>
59 59
60 <inputs> 60 <inputs>
61 <conditional name="formatType"> 61 <conditional name="formatType">
62 <param name="FormatInputFileName1" type="select" label="query File Format"> 62 <param name="FormatInputFileName1" type="select" label="query File Format">
115 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/> 115 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
116 </when> 116 </when>
117 </conditional> 117 </conditional>
118 118
119 <conditional name="OptionUpDownStream"> 119 <conditional name="OptionUpDownStream">
120 <param name="OptionUD" type="select" label="Only provide upstream/dowstream features"> 120 <param name="OptionUD" type="select" label="UpStream or DownStream">
121 <option value="UpStream">UpStream</option> 121 <option value="UpStream">UpStream</option>
122 <option value="DownStream">DownStream</option> 122 <option value="DownStream">DownStream</option>
123 <option value="NONE" selected="true">NONE</option> 123 <option value="NONE" selected="true">NONE</option>
124 </param> 124 </param>
125 <when value="UpStream"> 125 <when value="UpStream">
129 <when value="NONE"> 129 <when value="NONE">
130 </when> 130 </when>
131 </conditional> 131 </conditional>
132 132
133 <conditional name="OptionColinearOrAntiSens"> 133 <conditional name="OptionColinearOrAntiSens">
134 <param name="OptionCA" type="select" label="Only provide collinear/antisens features"> 134 <param name="OptionCA" type="select" label="Colinear or anti-sens">
135 <option value="Colinear">Collinear</option> 135 <option value="Colinear">Colinear</option>
136 <option value="AntiSens">AntiSens</option> 136 <option value="AntiSens">AntiSens</option>
137 <option value="NONE" selected="true">NONE</option> 137 <option value="NONE" selected="true">NONE</option>
138 </param> 138 </param>
139 <when value="Colinear"> 139 <when value="Colinear">
140 </when> 140 </when>
170 170
171 </inputs> 171 </inputs>
172 172
173 173
174 <outputs> 174 <outputs>
175 <data format="gff3" name="outputFile" label="[get flanking] output file"/> 175 <data format="gff3" name="outputFile" label="[GetFlanking] Output File"/>
176 </outputs> 176 </outputs>
177 177
178 <help>
179 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:
180
181 - restrict the search to downstream or upstream elements, or print downstream and upstream elements,
182
183 - only consider collinear flanking elements,
184
185 - only consider anti-sense flanking elements,
186
187 - only consider elements which are close enough (using some given distance),
188
189 - only consider flanking elements which do not overlap with the reference element.
190
191 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.
192 </help>
193 178
194 </tool> 179 </tool>