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comparison SMART/galaxy/mergeTranscriptLists.xml @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
1 <tool id="mergeTranscriptLists" name="merge transcript lists"> 1 <tool id="mergeTranscriptLists" name="merge transcript lists">
2 <description>Merge the elements of two lists of genomic coordinates.</description> 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"> 3 <command interpreter="python">
7 ../Java/Python/mergeTranscriptLists.py -i $formatType.inputFileName1 4 ../Java/Python/mergeTranscriptLists.py -i $formatType.inputFileName1
8 #if $formatType.FormatInputFileName1 == 'bed': 5 #if $formatType.FormatInputFileName1 == 'bed':
9 -f bed 6 -f bed
10 #elif $formatType.FormatInputFileName1 == 'gff': 7 #elif $formatType.FormatInputFileName1 == 'gff':
46 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens': 43 #elif $OptionColinearOrAntiSens.OptionCA == 'AntiSens':
47 -a 44 -a
48 #end if 45 #end if
49 46
50 -o $outputFileGff 47 -o $outputFileGff
48
49
50
51 </command> 51 </command>
52 52
53 <inputs> 53 <inputs>
54 <conditional name="formatType"> 54 <conditional name="formatType">
55 <param name="FormatInputFileName1" type="select" label="Input File Format 1"> 55 <param name="FormatInputFileName1" type="select" label="Input File Format 1">
140 </conditional> 140 </conditional>
141 141
142 </inputs> 142 </inputs>
143 143
144 <outputs> 144 <outputs>
145 <data name="outputFileGff" format="gff3" label="[merge transcript lists] output file"/> 145 <data name="outputFileGff" format="gff3" label="[mergeTranscriptLists]out file"/>
146 </outputs> 146 </outputs>
147 147
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> 148 </tool>