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5
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1 <tool id="proteinpilot_tabular" version="0.1" name="ProteinPilot - Convert Group to Tabular">
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0
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2 <description></description>
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5
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3 <!-- TOOD: Implement wrapper allowing Windows newlines to be replaced. -->
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0
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4 <command>
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5 #if $quant.use
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6 #set $denom = $quant.type
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7 #else
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8 #set $denom = ""
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9 #end if
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10 group2xml.exe ${type} $input $output $denom
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11 </command>
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12 <inputs>
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13 <param format="group" name="input" type="data" label="ProteinPilot Group Data" help=""/>
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14 <param name="type" type="select" label="Summary Type">
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15 <option value="PROTEIN">Protein</option>
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16 <option value="PEPTIDE">Peptide</option>
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17 </param>
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18 <conditional name="quant">
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19 <param name="use" type="boolean" label="Include quantation results" truevalue="true" falsevalue="false" />
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20 <when value="true">
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21 <param name="type" type="select" label="Denominator">
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22 <option value="IT113">113</option>
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23 <option value="IT114" selected="true">114</option>
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24 <option value="IT115">115</option>
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25 <option value="IT116">116</option>
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26 <option value="IT117">117</option>
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27 <option value="IT118">118</option>
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28 <option value="IT119">119</option>
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29 <option value="IT121">121</option>
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30 <option value="Light">Light</option>
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31 <option value="Heavy">Heavy</option>
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32 <option value="Medium">Medium</option>
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33 </param>
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34 </when>
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35 </conditional>
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36 </inputs>
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37 <outputs>
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38 <data format="tabular" name="output" label="${type} report for ${on_string}"/>
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39 </outputs>
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40 <help>
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41 </help>
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42 </tool>
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