Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/CompareOverlappingSmallQuery.xml @ 11:2da30502c2f1
Updated CompareOverlappingSmallQuery.xml
author | m-zytnicki |
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date | Thu, 14 Mar 2013 05:37:08 -0400 |
parents | 769e306b7933 |
children | 03045debed6e |
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10:c081f25e1572 | 11:2da30502c2f1 |
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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> |