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comparison SMART/galaxy/GetFlanking.xml @ 15:440ceca58672

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Uploaded
author m-zytnicki
date Mon, 22 Apr 2013 11:08:07 -0400
parents 769e306b7933
children 94ab73e8a190
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14:c79b9ae3f65f 15:440ceca58672
50 #if $OptionMin.minimum == "Yes": 50 #if $OptionMin.minimum == "Yes":
51 -d $OptionMin.min 51 -d $OptionMin.min
52 #end if 52 #end if
53 53
54 -o $outputFile 54 -o $outputFile
55
56
57
58 </command> 55 </command>
59 56
60 <inputs> 57 <inputs>
61 <conditional name="formatType"> 58 <conditional name="formatType">
62 <param name="FormatInputFileName1" type="select" label="query File Format"> 59 <param name="FormatInputFileName1" type="select" label="query File Format">
115 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/> 112 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
116 </when> 113 </when>
117 </conditional> 114 </conditional>
118 115
119 <conditional name="OptionUpDownStream"> 116 <conditional name="OptionUpDownStream">
120 <param name="OptionUD" type="select" label="UpStream or DownStream"> 117 <param name="OptionUD" type="select" label="Only provide upstream/dowstream features">
121 <option value="UpStream">UpStream</option> 118 <option value="UpStream">UpStream</option>
122 <option value="DownStream">DownStream</option> 119 <option value="DownStream">DownStream</option>
123 <option value="NONE" selected="true">NONE</option> 120 <option value="NONE" selected="true">NONE</option>
124 </param> 121 </param>
125 <when value="UpStream"> 122 <when value="UpStream">
129 <when value="NONE"> 126 <when value="NONE">
130 </when> 127 </when>
131 </conditional> 128 </conditional>
132 129
133 <conditional name="OptionColinearOrAntiSens"> 130 <conditional name="OptionColinearOrAntiSens">
134 <param name="OptionCA" type="select" label="Colinear or anti-sens"> 131 <param name="OptionCA" type="select" label="Only provide collinear/antisens features">
135 <option value="Colinear">Colinear</option> 132 <option value="Colinear">Collinear</option>
136 <option value="AntiSens">AntiSens</option> 133 <option value="AntiSens">AntiSens</option>
137 <option value="NONE" selected="true">NONE</option> 134 <option value="NONE" selected="true">NONE</option>
138 </param> 135 </param>
139 <when value="Colinear"> 136 <when value="Colinear">
140 </when> 137 </when>
173 170
174 <outputs> 171 <outputs>
175 <data format="gff3" name="outputFile" label="[GetFlanking] Output File"/> 172 <data format="gff3" name="outputFile" label="[GetFlanking] Output File"/>
176 </outputs> 173 </outputs>
177 174
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>
178 190
179 </tool> 191 </tool>