Mercurial > repos > yufei-luo > s_mart

comparison SMART/galaxy/CompareOverlappingSmallRef.xml @ 12:5a054da77808

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Updated CompareOverlappingSmallRef.xml
author m-zytnicki
date Thu, 14 Mar 2013 05:37:35 -0400
parents 769e306b7933
children 440ceca58672
comparison
equal deleted inserted replaced
11:2da30502c2f1 12:5a054da77808
31 #end if 31 #end if
32 -o $outputFileGff 32 -o $outputFileGff
33 #if $OptionDistance.Dist == 'Yes': 33 #if $OptionDistance.Dist == 'Yes':
34 -d $OptionDistance.distance 34 -d $OptionDistance.distance
35 #end if 35 #end if
36 #if $OptionColinearOrAntiSens.OptionCA == 'Colinear': 36 #if $OptionMinOverlap.present == 'Yes':
37 -m $OptionMinOverlap.minOverlap
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':
37 -c 46 -c
38 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens': 47 #elif $OptionCollinearOrAntiSens.OptionCA == 'AntiSens':
39 -a 48 -a
40 #end if 49 #end if
41 $InvertMatch 50 $InvertMatch
42 $NotOverlapping 51 $NotOverlapping
52 $OptionInclusionQuery
53 $OptionInclusionRef
43 </command> 54 </command>
44 55
45 <inputs> 56 <inputs>
46 <conditional name="formatType"> 57 <conditional name="formatType">
47 <param name="FormatInputFileName1" type="select" label="Input Query File Format"> 58 <param name="FormatInputFileName1" type="select" label="Input Query File Format">
109 <param name="distance" type="integer" value="0"/> 120 <param name="distance" type="integer" value="0"/>
110 </when> 121 </when>
111 <when value="No"> 122 <when value="No">
112 </when> 123 </when>
113 </conditional> 124 </conditional>
114 <conditional name="OptionColinearOrAntiSens"> 125 <conditional name="OptionMinOverlap">
115 <param name="OptionCA" type="select" label="Colinear or anti-sens"> 126 <param name="present" type="select" label="Minimum number of common nucleotides to declare an overlap">
116 <option value="Colinear">Colinear</option> 127 <option value="Yes">Yes</option>
128 <option value="No" selected="true">No</option>
129 </param>
130 <when value="Yes">
131 <param name="minOverlap" type="integer" value="0"/>
132 </when>
133 <when value="No">
134 </when>
135 </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">
161 <param name="OptionCA" type="select" label="Collinear or anti-sens">
162 <option value="Collinear">Collinear</option>
117 <option value="AntiSens">AntiSens</option> 163 <option value="AntiSens">AntiSens</option>
118 <option value="NONE" selected="true">NONE</option> 164 <option value="NONE" selected="true">NONE</option>
119 </param> 165 </param>
120 <when value="Colinear"> 166 <when value="Collinear">
121 </when> 167 </when>
122 <when value="AntiSens"> 168 <when value="AntiSens">
123 </when> 169 </when>
124 <when value="NONE"> 170 <when value="NONE">
125 </when> 171 </when>
126 </conditional> 172 </conditional>
127
128 <conditional name="OptionDistance">
129 <param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match"/> 173 <param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match"/>
130 <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."/> 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."/>
131 </conditional>
132 </inputs> 175 </inputs>
133 176
134 <outputs> 177 <outputs>
135 <data name="outputFileGff" format="gff3"/> 178 <data name="outputFileGff" format="gff3"/>
136 </outputs> 179 </outputs>