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1 <?xml version="1.0" ?>
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2 <tool id="qiime_gneiss_add-pseudocount" name="qiime gneiss add-pseudocount" version="2019.4">
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3 <description> - Add pseudocount to table</description>
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4 <requirements>
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5 <requirement type="package" version="2019.4">qiime2</requirement>
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6 </requirements>
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7 <command>
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8 <![CDATA[
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9 qiime gneiss add-pseudocount --i-table=$itable
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10
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11 #if $ppseudocount:
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12 --p-pseudocount=$ppseudocount
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13 #end if
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14
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15 #if str($cmdconfig) != 'None':
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16 --cmd-config=$cmdconfig
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17 #end if
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18 --o-composition-table=ocompositiontable;
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19
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20 cp ocompositiontable.qza $ocompositiontable
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21 ]]>
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22 </command>
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23 <inputs>
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24 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The feature table to which pseudocounts should be added. [required]" name="itable" optional="False" type="data"/>
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25 <param label="--p-pseudocount: The value to add to all counts in the feature table. [default: 1]" name="ppseudocount" optional="True" type="integer" value="1"/>
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26 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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27 </inputs>
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28 <outputs>
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29 <data format="qza" label="${tool.name} on ${on_string}: composition-table.qza" name="ocompositiontable"/>
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30 </outputs>
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31 <help>
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32 <![CDATA[
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33 Add pseudocount to table
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34 -------------------------
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35
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36 Increment all counts in table by pseudocount.
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37
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38 Parameters
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39 ----------
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40 table : FeatureTable[Frequency]
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41 The feature table to which pseudocounts should be added.
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42 pseudocount : Int, optional
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43 The value to add to all counts in the feature table.
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44
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45 Returns
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46 -------
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47 composition_table : FeatureTable[Composition]
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48 The resulting feature table.
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49 ]]>
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50 </help>
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51 <macros>
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52 <import>qiime_citation.xml</import>
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53 </macros>
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54 <expand macro="qiime_citation" />
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55 </tool>
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