Mercurial > repos > yufei-luo > s_mart

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

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Uploaded
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="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