Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/getDifference.xml @ 18:94ab73e8a190
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
parents | 440ceca58672 |
children | 0ab839023fe4 |
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17:b0e8584489e6 | 18:94ab73e8a190 |
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1 <tool id="getDifference" name="get Difference"> | 1 <tool id="getDifference" name="get difference"> |
2 <description>Gets all the regions of the genome, except the one given in an annotation file. Alternatively, it may also give all the elements from the first set which does not ovelap with the second set (at the nucleotide level).</description> | 2 <description>Gets all the regions of the genome, except the one given in an annotation file. Alternatively, it may also give all the elements from the first set which does not ovelap with the second set (at the nucleotide level).</description> |
3 <requirements> | |
4 <requirement type="set_environment">PYTHONPATH</requirement> | |
5 </requirements> | |
3 <command interpreter="python"> | 6 <command interpreter="python"> |
4 ../Java/Python/getDifference.py -i $formatType.inputFileName1 | 7 ../Java/Python/getDifference.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': |
117 | 120 |
118 </inputs> | 121 </inputs> |
119 | 122 |
120 | 123 |
121 <outputs> | 124 <outputs> |
122 <data name="outputFileGff" format="gff3" label="[getDifference]output File."/> | 125 <data name="outputFileGff" format="gff3" label="[get difference] output file."/> |
123 </outputs> | 126 </outputs> |
124 | 127 |
125 <help> | 128 <help> |
126 This tools has two different (but similar) uses. When given two sets of transcripts, it trims the elements of the set so that they do not overlap with the second set. | 129 This tools has two different (but similar) uses. When given two sets of transcripts, it trims the elements of the set so that they do not overlap with the second set. |
127 | 130 |