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1 <?xml version="1.0"?>
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2 <macros>
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3
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4 <xml name="sm_customisation">
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5 <section name="smcust" title="Sample metadata file coding parameters" expanded="False">
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6 <param name="batch_col_name" label="Batch column name" type="text" size="64" value="batch" help="The name of the column containing the batch values."/>
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7 <param name="injection_order_col_name" label="Injection order column name" type="text" size="64" value="injectionOrder" help="The name of the column containing the injection order values."/>
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8 <param name="sample_type_col_name" label="Sample type column name" type="text" size="64" value="sampleType" help="The name of the column containing the sample type values."/>
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9 <param name="sampleTypeTagPool" type="text" size="64" value="pool" label="Set the name used to tag samples as pool in the sample type column."/>
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10 <param name="sampleTypeTagBlank" type="text" size="64" value="blank" label="Set the name used to tag samples as blank in the sample type column."/>
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11 <param name="sampleTypeTagSample" type="text" size="64" value="sample" label="Set the name used to tag samples as real sample in the sample type column."/>
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12 </section>
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13 </xml>
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14
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15 <token name="@SM_CUSTOM@">
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16 batch_col_name "$smcust.batch_col_name"
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17 injection_order_col_name "$smcust.injection_order_col_name"
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18 sample_type_col_name "$smcust.sample_type_col_name"
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19 sample_type_tags "blank=$smcust.sampleTypeTagBlank,pool=$smcust.sampleTypeTagPool,sample=$smcust.sampleTypeTagSample"
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20 </token>
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21
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22 <xml name="foi">
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23 <param name="ref_factor" label="Factor of interest " type="text" value="batch" help="Column name of a factor of interest in the sampleMatadata table (if none, fill with the batch column name). Used for graphical display only; this factor does not affect correction calculation." />
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24 </xml>
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25
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26 <xml name="lll_span">
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27 <param name="span" type="float" value="1" label="span" help="It is an advanced option; strictly > 0 and maximum to 1."/>
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28 </xml>
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29
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30 <xml name="lll_options">
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31 <param name="valnull" label="Unconsistant values" type="select" display="radio" help="What to do of generated negative or infinite values">
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32 <option value="none">Prevent it: normalisation term reset to adequate minimum one</option>
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33 <option value="0">Consider it as a null intensity ('0')</option>
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34 <option value="NA">Consider it as a missing value ('NA')</option>
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35 </param>
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36 <expand macro="foi"/>
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37 <param name="detail" label="Level of details for plots " type="select" help="Amount of plots in the pdf file output. See Help section for more details.">
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38 <option value="no">basic</option>
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39 <option value="plot">standard</option>
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40 <option value="reg">complete</option>
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41 </param>
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42 </xml>
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43
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44 </macros>
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