Mercurial > repos > yufei-luo > s_mart

comparison SMART/galaxy/CompareOverlappingSmallQuery.xml @ 13:03045debed6e

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Uploaded
author m-zytnicki
date Wed, 17 Apr 2013 10:39:35 -0400
parents 2da30502c2f1
children 440ceca58672
comparison
equal deleted inserted replaced
12:5a054da77808 13:03045debed6e
34 -d $OptionDistance.distance 34 -d $OptionDistance.distance
35 #end if 35 #end if
36 #if $OptionMinOverlap.present == 'Yes': 36 #if $OptionMinOverlap.present == 'Yes':
37 -m $OptionMinOverlap.minOverlap 37 -m $OptionMinOverlap.minOverlap
38 #end if 38 #end if
39 #if $OptionPcOverlapQuery.present == 'Yes':
40 -p $OptionPcOverlapQuery.minOverlap
41 #end if
42 #if $OptionPcOverlapRef.present == 'Yes':
43 -P $OptionPcOverlapRef.minOverlap
44 #end if
45 #if $OptionCollinearOrAntiSens.OptionCA == 'Collinear': 39 #if $OptionCollinearOrAntiSens.OptionCA == 'Collinear':
46 -c 40 -c
47 #elif $OptionCollinearOrAntiSens.OptionCA == 'AntiSens': 41 #elif $OptionCollinearOrAntiSens.OptionCA == 'Antisense':
48 -a 42 -a
49 #end if 43 #end if
50 $InvertMatch 44 $InvertMatch
51 $NotOverlapping 45 $NotOverlapping
52 $OptionInclusionQuery
53 $OptionInclusionRef
54 </command> 46 </command>
55 47
56 <inputs> 48 <inputs>
57 <conditional name="formatType"> 49 <conditional name="formatType">
58 <param name="FormatInputFileName1" type="select" label="Input Query File Format"> 50 <param name="FormatInputFileName1" type="select" label="Input Query File Format">
110 <when value="gtf"> 102 <when value="gtf">
111 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/> 103 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
112 </when> 104 </when>
113 </conditional> 105 </conditional>
114 <conditional name="OptionDistance"> 106 <conditional name="OptionDistance">
115 <param name="Dist" type="select" label="Maximum Distance between two reads"> 107 <param name="Dist" type="select" label="Maximum Distance between two regions">
116 <option value="Yes">Yes</option> 108 <option value="Yes">Yes</option>
117 <option value="No" selected="true">No</option> 109 <option value="No" selected="true">No</option>
118 </param> 110 </param>
119 <when value="Yes"> 111 <when value="Yes">
120 <param name="distance" type="integer" value="0"/> 112 <param name="distance" type="integer" value="0"/>
131 <param name="minOverlap" type="integer" value="0"/> 123 <param name="minOverlap" type="integer" value="0"/>
132 </when> 124 </when>
133 <when value="No"> 125 <when value="No">
134 </when> 126 </when>
135 </conditional> 127 </conditional>
136 <conditional name="OptionPcOverlapQuery">
137 <param name="present" type="select" label="N% of the query must overlap">
138 <option value="Yes">Yes</option>
139 <option value="No" selected="true">No</option>
140 </param>
141 <when value="Yes">
142 <param name="minOverlap" type="integer" value="0"/>
143 </when>
144 <when value="No">
145 </when>
146 </conditional>
147 <conditional name="OptionPcOverlapRef">
148 <param name="present" type="select" label="N% of the reference must overlap">
149 <option value="Yes">Yes</option>
150 <option value="No" selected="true">No</option>
151 </param>
152 <when value="Yes">
153 <param name="minOverlap" type="integer" value="0"/>
154 </when>
155 <when value="No">
156 </when>
157 </conditional>
158 <param name="OptionInclusionQuery" type="boolean" truevalue="-k" falsevalue="" checked="false" label="The query must nested in a query"/>
159 <param name="OptionInclusionRef" type="boolean" truevalue="-K" falsevalue="" checked="false" label="The reference must nested in a query"/>
160 <conditional name="OptionCollinearOrAntiSens"> 128 <conditional name="OptionCollinearOrAntiSens">
161 <param name="OptionCA" type="select" label="Collinear or anti-sens"> 129 <param name="OptionCA" type="select" label="Collinear or Antisense">
162 <option value="Collinear">Collinear</option> 130 <option value="Collinear">Collinear</option>
163 <option value="AntiSens">AntiSens</option> 131 <option value="Antisense">Antisense</option>
164 <option value="NONE" selected="true">NONE</option> 132 <option value="NONE" selected="true">NONE</option>
165 </param> 133 </param>
166 <when value="Collinear"> 134 <when value="Collinear">
167 </when> 135 </when>
168 <when value="AntiSens"> 136 <when value="Antisense">
169 </when> 137 </when>
170 <when value="NONE"> 138 <when value="NONE">
171 </when> 139 </when>
172 </conditional> 140 </conditional>
173 <param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match"/> 141 <param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match"/>
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."/> 142 <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 default."/>
175 </inputs> 143 </inputs>
176 144
177 <outputs> 145 <outputs>
178 <data name="outputFileGff" format="gff3"/> 146 <data name="outputFileGff" format="gff3"/>
179 </outputs> 147 </outputs>