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1 <tool id="DESEQ" name="DESEQ for differential expression analysis">
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2 <description>Differential expression analysis for reads count data</description>
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3 <command interpreter="bash"> deseq.sh $inputFile $header $withOutReplicates $outHTML $outHTML.files_path $outComplete $outUP $outDown 2> $log </command>
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4
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5 <inputs>
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6 <param name="inputFile" type="data" label="Input File list" format="txt"/>
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7 <param name="header" type="boolean" truevalue="1" falsevalue="0" checked="false" label="If there is a header for your count files, please choose this case."/>
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8 <param name="withOutReplicates" type="boolean" truevalue="1" falsevalue="0" checked="false" label="If your data has not replicates, please choose this case."/>
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9
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10 </inputs>
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11
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12 <outputs>
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13 <data format="HTML" name="outHTML" label="[DESEQ] Output HTML File" help="This output file shows all results images by DESeq analysis"/>
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14 <data format="tabular" name="outComplete" label="[DESEQ] Output complete File"/>
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15 <data format="tabular" name="outUP" label="[DESEQ] Output up File" help="This output file shows the genes of group1 which are overexpressed than those of group2"/>
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16 <data format="tabular" name="outDown" label="[DESEQ] Output down File" help="This output file shows the genes of group1 which are less expressed than those of group2"/>
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17 <data format="txt" name="log" label="[DESEQ] Output log File"/>
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18 </outputs>
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19
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20 <help>
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21 </help>
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22 </tool>
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