38
+ − 1 <tool id="mergeTranscriptLists" name="merge transcript lists">
+ − 2 <description>Merge the elements of two lists of genomic coordinates.</description>
+ − 3 <requirements>
+ − 4 <requirement type="set_environment">PYTHONPATH</requirement>
+ − 5 </requirements>
+ − 6 <command interpreter="python">
+ − 7 ../Java/Python/mergeTranscriptLists.py -i $formatType.inputFileName1
+ − 8 #if $formatType.FormatInputFileName1 == 'bed':
+ − 9 -f bed
+ − 10 #elif $formatType.FormatInputFileName1 == 'gff':
+ − 11 -f gff
+ − 12 #elif $formatType.FormatInputFileName1 == 'gff2':
+ − 13 -f gff2
+ − 14 #elif $formatType.FormatInputFileName1 == 'gff3':
+ − 15 -f gff3
+ − 16 #elif $formatType.FormatInputFileName1 == 'sam':
+ − 17 -f sam
+ − 18 #elif $formatType.FormatInputFileName1 == 'gtf':
+ − 19 -f gtf
+ − 20 #end if
+ − 21
+ − 22 -j $formatType2.inputFileName2
+ − 23 #if $formatType2.FormatInputFileName2 == 'bed':
+ − 24 -g bed
+ − 25 #elif $formatType2.FormatInputFileName2 == 'gff':
+ − 26 -g gff
+ − 27 #elif $formatType2.FormatInputFileName2 == 'gff2':
+ − 28 -g gff2
+ − 29 #elif $formatType2.FormatInputFileName2 == 'gff3':
+ − 30 -g gff3
+ − 31 #elif $formatType2.FormatInputFileName2 == 'sam':
+ − 32 -g sam
+ − 33 #elif $formatType2.FormatInputFileName2 == 'gtf':
+ − 34 -g gtf
+ − 35 #end if
+ − 36
+ − 37 $all
+ − 38 $normalize
+ − 39
+ − 40 #if $OptionDistance.dis == 'Yes':
+ − 41 -d $OptionDistance.disVal
+ − 42 #end if
+ − 43
+ − 44 #if $OptionColinearOrAntiSens.OptionCA == 'Colinear':
+ − 45 -c
+ − 46 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
+ − 47 -a
+ − 48 #end if
+ − 49
+ − 50 -o $outputFileGff
+ − 51 </command>
+ − 52
+ − 53 <inputs>
+ − 54 <conditional name="formatType">
+ − 55 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
+ − 56 <option value="bed">bed</option>
+ − 57 <option value="gff">gff</option>
+ − 58 <option value="gff2">gff2</option>
+ − 59 <option value="gff3">gff3</option>
+ − 60 <option value="sam">sam</option>
+ − 61 <option value="gtf">gtf</option>
+ − 62 </param>
+ − 63 <when value="bed">
+ − 64 <param name="inputFileName1" format="bed" type="data" label="Input File 1"/>
+ − 65 </when>
+ − 66 <when value="gff">
+ − 67 <param name="inputFileName1" format="gff" type="data" label="Input File 1"/>
+ − 68 </when>
+ − 69 <when value="gff2">
+ − 70 <param name="inputFileName1" format="gff2" type="data" label="Input File 1"/>
+ − 71 </when>
+ − 72 <when value="gff3">
+ − 73 <param name="inputFileName1" format="gff3" type="data" label="Input File 1"/>
+ − 74 </when>
+ − 75 <when value="sam">
+ − 76 <param name="inputFileName1" format="sam" type="data" label="Input File 1"/>
+ − 77 </when>
+ − 78 <when value="gtf">
+ − 79 <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/>
+ − 80 </when>
+ − 81 </conditional>
+ − 82
+ − 83 <conditional name="formatType2">
+ − 84 <param name="FormatInputFileName2" type="select" label="Input File Format 2">
+ − 85 <option value="bed">bed</option>
+ − 86 <option value="gff">gff</option>
+ − 87 <option value="gff2">gff2</option>
+ − 88 <option value="gff3">gff3</option>
+ − 89 <option value="sam">sam</option>
+ − 90 <option value="gtf">gtf</option>
+ − 91 </param>
+ − 92 <when value="bed">
+ − 93 <param name="inputFileName2" format="bed" type="data" label="Input File 2"/>
+ − 94 </when>
+ − 95 <when value="gff">
+ − 96 <param name="inputFileName2" format="gff" type="data" label="Input File 2"/>
+ − 97 </when>
+ − 98 <when value="gff2">
+ − 99 <param name="inputFileName2" format="gff2" type="data" label="Input File 2"/>
+ − 100 </when>
+ − 101 <when value="gff3">
+ − 102 <param name="inputFileName2" format="gff3" type="data" label="Input File 2"/>
+ − 103 </when>
+ − 104 <when value="sam">
+ − 105 <param name="inputFileName2" format="sam" type="data" label="Input File 2"/>
+ − 106 </when>
+ − 107 <when value="gtf">
+ − 108 <param name="inputFileName2" format="gtf" type="data" label="Input File 2"/>
+ − 109 </when>
+ − 110 </conditional>
+ − 111
+ − 112
+ − 113 <param name="all" type="boolean" truevalue="-k" falsevalue="" checked="false" label="print all the transcripts, not only those overlapping"/>
+ − 114 <param name="normalize" type="boolean" truevalue="-n" falsevalue="" checked="false" label="normalize the number of reads per cluster by the number of mappings per read "/>
+ − 115
+ − 116 <conditional name="OptionDistance">
+ − 117 <param name="dis" type="select" label="provide the number of reads" >
+ − 118 <option value="Yes">Yes</option>
+ − 119 <option value="No" selected="true">No</option>
+ − 120 </param>
+ − 121 <when value="Yes">
+ − 122 <param name="disVal" type="integer" value="0" label="max. distance between two transcripts" />
+ − 123 </when>
+ − 124 <when value="No">
+ − 125 </when>
+ − 126 </conditional>
+ − 127
+ − 128 <conditional name="OptionColinearOrAntiSens">
+ − 129 <param name="OptionCA" type="select" label="Colinear or anti-sens">
+ − 130 <option value="Colinear">Colinear</option>
+ − 131 <option value="AntiSens">AntiSens</option>
+ − 132 <option value="NONE" selected="true">NONE</option>
+ − 133 </param>
+ − 134 <when value="Colinear">
+ − 135 </when>
+ − 136 <when value="AntiSens">
+ − 137 </when>
+ − 138 <when value="NONE">
+ − 139 </when>
+ − 140 </conditional>
+ − 141
+ − 142 </inputs>
+ − 143
+ − 144 <outputs>
+ − 145 <data name="outputFileGff" format="gff3" label="[merge transcript lists] output file"/>
+ − 146 </outputs>
+ − 147
+ − 148 <help>
+ − 149 The script is similar to *compare overlapping*, except that when data of two different sets overlap, they are merged. You can use the same parameters as *compare overlapping* and use them to look for transcription on both strands, for example.
+ − 150
+ − 151 Optionally, you can also add to the output all the elements from the first set which do not overlap with the second set.
+ − 152 </help>
+ − 153 </tool>
