Mercurial > repos > yufei-luo > s_mart

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

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Uploaded
author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
parents 440ceca58672
children 0ab839023fe4
comparison
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17:b0e8584489e6 18:94ab73e8a190
1 <tool id="restrictTranscriptList" name="restrict transcript list"> 1 <tool id="restrictTranscriptList" name="restrict transcript list">
2 <description>Select the features which are located in a given locus.</description> 2 <description>Select the features which are located in a given locus.</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
3 <command interpreter="python"> ../Java/Python/restrictTranscriptList.py -i $formatType.inputFileName 6 <command interpreter="python"> ../Java/Python/restrictTranscriptList.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
98 </when> 101 </when>
99 </conditional> 102 </conditional>
100 </inputs> 103 </inputs>
101 104
102 <outputs> 105 <outputs>
103 <data format="gff3" name="outputFile" label="[restrictTranscriptList] Output File"/> 106 <data format="gff3" name="outputFile" label="[restrict transcript list] output file"/>
104 </outputs> 107 </outputs>
105 108
106 <help> 109 <help>
110 Reads a list of genomic coordinates and outputs those which on a given chromosome and / or between two given positions.
107 </help> 111 </help>
108 <tests> 112 <tests>
109 <test> 113 <test>
110 <param name="FormatInputFileName" value="gtf" /> 114 <param name="FormatInputFileName" value="gtf" />
111 <param name="inputFileName" value="genes.gtf" /> 115 <param name="inputFileName" value="genes.gtf" />
115 <param name="end" value="No" /> 119 <param name="end" value="No" />
116 <output name="outputFile" file="exp_restrictTranscriptList.gff3" /> 120 <output name="outputFile" file="exp_restrictTranscriptList.gff3" />
117 </test> 121 </test>
118 </tests> 122 </tests>
119 123
120 <help>
121 Reads a list of genomic coordinates and outputs those which on a given chromosome and / or between two given positions.
122 </help>
123
124 </tool> 124 </tool>