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1 <tool id="EdgeR_differentialExpression" name="EdgeR_differentialExpression" version="0.0.1">
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2
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3 <description>Identify Differentially Expressed Transcripts Using EdgeR</description>
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4 <requirements>
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5 <requirement type="package">trinity</requirement>
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6 </requirements>
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7 <command interpreter="python">
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8
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9 EdgeR_differentialExpression_wrapper.py
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10 $counts_matrix
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11 $dispersion
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12
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13 </command>
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14 <inputs>
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15
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16 <param type="data" format="txt" name="counts_matrix" label="Matrix of RNA-Seq fragment counts for transcripts per condition" />
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17 <param type="data" format="fasta" name="transcripts_fasta_file" label="Transcripts fasta file corresponding to matrix" />
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18 <param type="float" name="dispersion" value="0.1" min="0" label="dispersion value" help="Dispersion value to be used in the negative binomial" />
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19
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20 </inputs>
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21 <outputs>
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22
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23 <data format="tar.gz" name="EdgeR_Archive" label="${tool.name} on ${on_string}: EdgeR_Results.tar.gz" from_work_dir="edgeR_results.tar.gz" />
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24
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25 </outputs>
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26 <tests>
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27
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28 <test>
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29 <param name="myname" value="This is just a simple test" />
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30
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31 </test>
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32
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33
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34 </tests>
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35 <help>
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36 help info here.
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37 </help>
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38 </tool>
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