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comparison SMART/galaxy/mergeTranscriptLists.xml @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
parents 440ceca58672
children 0ab839023fe4
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17:b0e8584489e6 18:94ab73e8a190
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>
3 <command interpreter="python"> 6 <command interpreter="python">
4 ../Java/Python/mergeTranscriptLists.py -i $formatType.inputFileName1 7 ../Java/Python/mergeTranscriptLists.py -i $formatType.inputFileName1
5 #if $formatType.FormatInputFileName1 == 'bed': 8 #if $formatType.FormatInputFileName1 == 'bed':
6 -f bed 9 -f bed
7 #elif $formatType.FormatInputFileName1 == 'gff': 10 #elif $formatType.FormatInputFileName1 == 'gff':
137 </conditional> 140 </conditional>
138 141
139 </inputs> 142 </inputs>
140 143
141 <outputs> 144 <outputs>
142 <data name="outputFileGff" format="gff3" label="[mergeTranscriptLists]out file"/> 145 <data name="outputFileGff" format="gff3" label="[merge transcript lists] output file"/>
143 </outputs> 146 </outputs>
144 147
145 <help> 148 <help>
146 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. 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.
147 150