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1 <tool id="compare_targets" name="Compare Targets" version="1.3.1">
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2 <description>Post-processing analysis: compares the target genes from two EMBER runs</description>
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3 <command interpreter="perl">Compare_Targets.pl -t1 $set1 -t2 $set2 -o $output -of $outtype -n $comptype</command>
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4 <inputs>
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5 <param format="txt" name="set1" type="data" label="Targets file 1"/>
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6 <param format="txt" name="set2" type="data" label="Targets file 2"/>
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7 <param name="outtype" type="select" label="Output type">
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8 <option value="0" selected="true">All shared targets</option>
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9 <option value="1">Targets unique to file 1</option>
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10 <option value="2">Targets unique to file 2</option>
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11 <option value="3">Union of targets from files 1 and 2</option>
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12 </param>
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13 <param name="comptype" type="select" label="Value to compare">
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14 <option value="1" selected="true">Gene names</option>
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15 <option value="0">Probe set IDs</option>
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16 </param>
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17 </inputs>
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18 <outputs>
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19 <data format="txt" name="output"/>
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20 </outputs>
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21
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22 <tests>
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23 <test>
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24 <param name="set1" value="EMBER/patterns-1.targets"/>
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25 <param name="set2" value="EMBER/patterns-1.targets"/>
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26 <param name="outtype" value="0"/>
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27 <param name="comptype" value="1"/>
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28 <output name="output" file="EMBER/targets_1-1.txt"/>
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29 </test>
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30 </tests>
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31
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32
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33 <help>
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34
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35 This tool compares the list of gene targets from different EMBER runs.
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36
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37 -----
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38
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39 Description of inputs:
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40
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41 *Targets files 1 and 2*: the .targets outputs of EMBER (lines start with "PEAK:" or "TGENE:").
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42
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43 *Output type*: This tool compares the gene sets, and you can choose which comparison to print, either the intersection, difference, or union.
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44
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45 *Value to compare*: Choose gene name or probe set ID; some genes have multiple probe sets.
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46
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47 </help>
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48
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49 </tool>
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50
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