31
+ − 1 <tool id="CompareOverlappingSmallQuery" name="Compare Overlapping Small Query">
+ − 2 <description>Provide the queries that overlap with a reference, when the query is small.</description>
6
+ − 3 <command interpreter="python">
+ − 4 ../Java/Python/CompareOverlappingSmallQuery.py -i $formatType.inputFileName1
+ − 5 #if $formatType.FormatInputFileName1 == 'bed':
+ − 6 -f bed
+ − 7 #elif $formatType.FormatInputFileName1 == 'gff':
+ − 8 -f gff
+ − 9 #elif $formatType.FormatInputFileName1 == 'gff2':
+ − 10 -f gff2
+ − 11 #elif $formatType.FormatInputFileName1 == 'gff3':
+ − 12 -f gff3
+ − 13 #elif $formatType.FormatInputFileName1 == 'sam':
+ − 14 -f sam
+ − 15 #elif $formatType.FormatInputFileName1 == 'gtf':
+ − 16 -f gtf
+ − 17 #end if
+ − 18 -j $formatType2.inputFileName2
+ − 19 #if $formatType2.FormatInputFileName2 == 'bed':
+ − 20 -g bed
+ − 21 #elif $formatType2.FormatInputFileName2 == 'gff':
+ − 22 -g gff
+ − 23 #elif $formatType2.FormatInputFileName2 == 'gff2':
+ − 24 -g gff2
+ − 25 #elif $formatType2.FormatInputFileName2 == 'gff3':
+ − 26 -g gff3
+ − 27 #elif $formatType2.FormatInputFileName2 == 'sam':
+ − 28 -g sam
+ − 29 #elif $formatType2.FormatInputFileName2 == 'gtf':
+ − 30 -g gtf
+ − 31 #end if
+ − 32 -o $outputFileGff
+ − 33 #if $OptionDistance.Dist == 'Yes':
+ − 34 -d $OptionDistance.distance
+ − 35 #end if
11
+ − 36 #if $OptionMinOverlap.present == 'Yes':
+ − 37 -m $OptionMinOverlap.minOverlap
+ − 38 #end if
15
+ − 39 #if $OptionPcOverlapQuery.present == 'Yes':
+ − 40 -p $OptionPcOverlapQuery.minOverlap
+ − 41 #end if
+ − 42 #if $OptionPcOverlapRef.present == 'Yes':
+ − 43 -P $OptionPcOverlapRef.minOverlap
+ − 44 #end if
11
+ − 45 #if $OptionCollinearOrAntiSens.OptionCA == 'Collinear':
6
+ − 46 -c
15
+ − 47 #elif $OptionCollinearOrAntiSens.OptionCA == 'AntiSens':
6
+ − 48 -a
+ − 49 #end if
+ − 50 $InvertMatch
+ − 51 $NotOverlapping
15
+ − 52 $OptionInclusionQuery
+ − 53 $OptionInclusionRef
6
+ − 54 </command>
+ − 55
+ − 56 <inputs>
+ − 57 <conditional name="formatType">
+ − 58 <param name="FormatInputFileName1" type="select" label="Input Query File Format">
+ − 59 <option value="bed">bed</option>
+ − 60 <option value="gff">gff</option>
+ − 61 <option value="gff2">gff2</option>
+ − 62 <option value="gff3">gff3</option>
+ − 63 <option value="sam">sam</option>
+ − 64 <option value="gtf">gtf</option>
+ − 65 </param>
+ − 66 <when value="bed">
+ − 67 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
+ − 68 </when>
+ − 69 <when value="gff">
+ − 70 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
+ − 71 </when>
+ − 72 <when value="gff2">
+ − 73 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
+ − 74 </when>
+ − 75 <when value="gff3">
+ − 76 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
+ − 77 </when>
+ − 78 <when value="sam">
+ − 79 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
+ − 80 </when>
+ − 81 <when value="gtf">
+ − 82 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
+ − 83 </when>
+ − 84 </conditional>
+ − 85
+ − 86 <conditional name="formatType2">
+ − 87 <param name="FormatInputFileName2" type="select" label="Input Reference File Format">
+ − 88 <option value="bed">bed</option>
+ − 89 <option value="gff">gff</option>
+ − 90 <option value="gff2">gff2</option>
+ − 91 <option value="gff3">gff3</option>
+ − 92 <option value="sam">sam</option>
+ − 93 <option value="gtf">gtf</option>
+ − 94 </param>
+ − 95 <when value="bed">
+ − 96 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
+ − 97 </when>
+ − 98 <when value="gff">
+ − 99 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
+ − 100 </when>
+ − 101 <when value="gff2">
+ − 102 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
+ − 103 </when>
+ − 104 <when value="gff3">
+ − 105 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
+ − 106 </when>
+ − 107 <when value="sam">
+ − 108 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
+ − 109 </when>
+ − 110 <when value="gtf">
+ − 111 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
+ − 112 </when>
+ − 113 </conditional>
+ − 114 <conditional name="OptionDistance">
15
+ − 115 <param name="Dist" type="select" label="Maximum Distance between two reads">
6
+ − 116 <option value="Yes">Yes</option>
+ − 117 <option value="No" selected="true">No</option>
+ − 118 </param>
+ − 119 <when value="Yes">
+ − 120 <param name="distance" type="integer" value="0"/>
+ − 121 </when>
+ − 122 <when value="No">
+ − 123 </when>
+ − 124 </conditional>
11
+ − 125 <conditional name="OptionMinOverlap">
+ − 126 <param name="present" type="select" label="Minimum number of common nucleotides to declare an overlap">
+ − 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>
15
+ − 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>
31
+ − 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"/>
11
+ − 160 <conditional name="OptionCollinearOrAntiSens">
15
+ − 161 <param name="OptionCA" type="select" label="Collinear or anti-sens">
11
+ − 162 <option value="Collinear">Collinear</option>
15
+ − 163 <option value="AntiSens">AntiSens</option>
6
+ − 164 <option value="NONE" selected="true">NONE</option>
+ − 165 </param>
11
+ − 166 <when value="Collinear">
6
+ − 167 </when>
15
+ − 168 <when value="AntiSens">
6
+ − 169 </when>
+ − 170 <when value="NONE">
+ − 171 </when>
+ − 172 </conditional>
31
+ − 173 <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."/>
6
+ − 175 </inputs>
+ − 176
+ − 177 <outputs>
+ − 178 <data name="outputFileGff" format="gff3"/>
+ − 179 </outputs>
+ − 180 </tool>
