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comparison EBIsoformTwoCondTest.xml @ 22:b2462f571961 draft

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author ning
date Wed, 20 Mar 2013 00:08:06 -0400
parents 7218b8ff560e
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21:72d5e182774f 22:b2462f571961
1 <tool id="EBIsoformTwoCondTest" name="Isoform level DE test across two conditions"> 1 <tool id="EBIsoformTwoCondTest" name="Isoform level DE test across two conditions">
2 <description>Runs EBSeq to find DE isoforms across two conditions</description> 2 <description>Runs EBSeq to find DE isoforms across two conditions</description>
3 <command>R --quiet --slave --file=$GALAXY_ROOT_DIR/tools/EBSeq/EBIsoformTwoCondTest.R --args $Isoform_Expression $First_Row_Sample_Names $Conditions $Ig_Vector $Target_FDR $Output $Sorted_Output $Sorted_Outpu_with_target_FDR $Sizes</command> 3 <command>R --quiet --slave --file=$GALAXY_ROOT_DIR/tools/EBSeq/EBIsoformTwoCondTest.R --args $Isoform_Expression $First_Row_Sample_Names $Conditions $Ig_Vector $Target_FDR $Output $Sorted_Output $Sorted_Outpu_with_target_FDR $Sizes</command>
4 <inputs> 4 <inputs>
5 <param name="Isoform_Expression" type="data" format="tabular" label="Isoform Expression (tab eliminated, please use the unnormalized values)"/> 5 <param name="Isoform_Expression" type="data" format="tabular" label="Isoform Expression (tab delimited, please use the unnormalized values, e.g. expected counts form RSEM)"/>
6 <param name="First_Row_Sample_Names" type="select" format="text"> 6 <param name="First_Row_Sample_Names" type="select" format="text">
7 <label>The First Row is Sample Names?</label> 7 <label>The First Row is Sample Names?</label>
8 <option value="y">Yes</option> 8 <option value="y">Yes</option>
9 <option value="n">No</option> 9 <option value="n">No</option>
10 </param> 10 </param>
11 <param name="Conditions" type="text" size="60" value="C1,C2" label="Enter which condition each 11 <param name="Conditions" type="text" size="60" value="C1,C2" label="Enter which condition each
12 sample belongs to (seperated by comma, no space please)." 12 sample belongs to (separated by comma, no space please)."
13 help=""/> 13 help=""/>
14 <param name="Ig_Vector" type="data" format="tabular" label="Ig Vector to define the uncertainty groups"/> 14 <param name="Ig_Vector" type="data" format="tabular" label="Ig Vector to define the uncertainty groups"/>
15 <param name="Target_FDR" type="text" format="tabular" value="0.05" label="Target FDR" 15 <param name="Target_FDR" type="text" format="tabular" value="0.05" label="Target FDR"
16 /> 16 />
17 </inputs> 17 </inputs>