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comparison SMART/galaxy/modifyGenomicCoordinates.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="modifyGenomicCoordinates" name="modify genomic coordinates"> 1 <tool id="modifyGenomicCoordinates" name="modify genomic coordinates">
2 <description>Extend or shrink a list of genomic coordinates.</description> 2 <description>Extend or shrink a list of genomic coordinates.</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
3 <command interpreter="python"> ../Java/Python/modifyGenomicCoordinates.py -i $formatType.inputFileName 6 <command interpreter="python"> ../Java/Python/modifyGenomicCoordinates.py -i $formatType.inputFileName
4 #if $formatType.FormatInputFileName == 'bed': 7 #if $formatType.FormatInputFileName == 'bed':
5 -f bed 8 -f bed
6 #elif $formatType.FormatInputFileName == 'gff': 9 #elif $formatType.FormatInputFileName == 'gff':
7 -f gff 10 -f gff
116 119
117 120
118 </inputs> 121 </inputs>
119 122
120 <outputs> 123 <outputs>
121 <data format="gff3" name="outputFile" label="[modifyGenomicCoordinates] Output File"/> 124 <data format="gff3" name="outputFile" label="[modify genomic coordinates] output file"/>
122 </outputs> 125 </outputs>
123 126
124 <help> 127 <help>
125 This tool reads a list of transcripts and modifies each feature by: 128 This tool reads a list of transcripts and modifies each feature by:
126 129
127 - shrinking it to the $ n $ first nucleotides or the *n* last nucleotides, or 130 - shrinking it to the *n* first nucleotides or the *n* last nucleotides, or
128 131
129 - extending it to $ n $ nucleotides towards the 5' direction (upstream) or the 3' direction (downstream). 132 - extending it to *n* nucleotides towards the 5' direction (upstream) or the 3' direction (downstream).
130 133
131 Note that the 5' or 3' direction depends on the orientation of the feature (the 5' end of a transcript located on the minus strand is on the right hand of this transcript!). 134 Note that the 5' or 3' direction depends on the orientation of the feature (the 5' end of a transcript located on the minus strand is on the right hand of this transcript!).
132 135
133 The tool needs a transcript file, its format, and outputs a new transcript file. 136 The tool needs a transcript file, its format, and outputs a new transcript file.
134 </help> 137 </help>