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comparison SMART/galaxy/CompareOverlappingSmallQuery.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="CompareOverlappingSmallQuery" name="compare overlapping small query"> 1 <tool id="CompareOverlappingSmallQuery" name="Compare Overlapping Small Query">
2 <description>Provide the queries that overlap with a reference, when the query data set is small.</description> 2 <description>Provide the queries that overlap with a reference, when the query is small.</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python"> 3 <command interpreter="python">
7 ../Java/Python/CompareOverlappingSmallQuery.py -i $formatType.inputFileName1 4 ../Java/Python/CompareOverlappingSmallQuery.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':
156 <param name="minOverlap" type="integer" value="0"/> 153 <param name="minOverlap" type="integer" value="0"/>
157 </when> 154 </when>
158 <when value="No"> 155 <when value="No">
159 </when> 156 </when>
160 </conditional> 157 </conditional>
161 <param name="OptionInclusionQuery" type="boolean" truevalue="-k" falsevalue="" checked="false" label="The query must be nested in a query"/> 158 <param name="OptionInclusionQuery" type="boolean" truevalue="-k" falsevalue="" checked="false" label="The query must nested in a query"/>
162 <param name="OptionInclusionRef" type="boolean" truevalue="-K" falsevalue="" checked="false" label="The reference must be nested in a query"/> 159 <param name="OptionInclusionRef" type="boolean" truevalue="-K" falsevalue="" checked="false" label="The reference must nested in a query"/>
163 <conditional name="OptionCollinearOrAntiSens"> 160 <conditional name="OptionCollinearOrAntiSens">
164 <param name="OptionCA" type="select" label="Collinear or anti-sens"> 161 <param name="OptionCA" type="select" label="Collinear or anti-sens">
165 <option value="Collinear">Collinear</option> 162 <option value="Collinear">Collinear</option>
166 <option value="AntiSens">AntiSens</option> 163 <option value="AntiSens">AntiSens</option>
167 <option value="NONE" selected="true">NONE</option> 164 <option value="NONE" selected="true">NONE</option>
171 <when value="AntiSens"> 168 <when value="AntiSens">
172 </when> 169 </when>
173 <when value="NONE"> 170 <when value="NONE">
174 </when> 171 </when>
175 </conditional> 172 </conditional>
176 <param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match: the output file will contain all query elements which do NOT overlap"/> 173 <param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match"/>
177 <param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="Also report the query data which do not overlap, with the nbOverlaps tag set to 0."/> 174 <param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="When there is no overlapping, the number of Overlapping will be set to 0 by defalt."/>
178 </inputs> 175 </inputs>
179 176
180 <outputs> 177 <outputs>
181 <data name="outputFileGff" format="gff3"/> 178 <data name="outputFileGff" format="gff3"/>
182 </outputs> 179 </outputs>
183
184 <help>
185 This script may be the most important one. It basically compares two sets of transcripts and keeps those from the first set which overlap with the second one. The first set is considered as the query set (basically, your data) and the second one is the reference set (RefSeq data, for example).
186
187 It is vital to understand that it will output the elements of the first file which overlap with the elements of the second one.
188
189 Various modifiers are also available:
190
191 -Invert selection (report those which do not overlap).
192
193 -Restrict to colinear / anti-sense overlapping data.
194
195 -Keep the query data even if they do not strictly overlap with the reference data, but are located not further away than *n* nucleotide from some reference data.
196
197 -Keep the query data with are strictly included into reference data, meaning that a query transcript such that at least 1 nucleotide does not overlap with reference data will not be presented as a solution.
198
199 The mechanism of shrinking and extending is also useful to make a fine grain comparison. For example, if you want to keep those such that the TSS is overlapping the reference set, you just shrink the query set to 1 nucleotide. Now, if you want to keep those which are overlapping you data or located 2kb downstream of it, just extend the query data in the downstream direction, and you will have what you want. You can also extend in the opposite direction to get the possible transcript factor sites which are upstream.
200
201 Some option reverses the selection. Put in other words, it performs the comparison as usual, and outputs all those query data which do not overlap.
202 </help>
203 </tool> 180 </tool>