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1 <tool id="PHYLO_bootstrap" name="Prepare data" version="1.1.0">
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2 <description>for analysis</description>
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6
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package">yapp_env</requirement>
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8 </requirements>
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6
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9 <stdio>
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10 <expand macro="basic_errors"/>
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11 </stdio>
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12 <version_command>echo "bootstrap script 1.1.0"</version_command>
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13 <command interpreter="bash">
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14 bootstrap-wrapper.sh $config
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15 </command>
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16 <inputs>
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17 <param name="plate_id" type="integer" value="1" label="Plate number"/>
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18 <conditional name="run_type">
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19 <param name="run_type_select" type="select" label="Run type">
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20 <option value="junior">Junior</option>
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21 <option value="senior">Senior</option>
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22 </param>
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23 <when value="junior"></when>
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24 <when value="senior">
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25 <param name="zone_id" type="integer" value="1" label="Zone number"/>
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26 </when>
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27 </conditional>
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28 <param name="sample_info" type="data" format="csv" label="Sample information"/>
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29 </inputs>
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30 <outputs>
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31 <data format="csv" name="barcodes" label="Specimen-to-barcode map"/>
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32 <data format="csv" name="labels" label="Specimen-to-label map"/>
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33 <data format="csv" name="metadata" label="Metadata template"/>
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34 </outputs>
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35 <configfiles>
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36 <configfile name="config">
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37 PLATE_ID="${plate_id}"
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38 #if $run_type.run_type_select == "senior"
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39 JUNIOR=""
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40 ZONE_ID="${run_type.zone_id}"
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41 #else
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42 JUNIOR="--junior"
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43 ZONE_ID="1"
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44 #end if
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45 SAMPLE_INFO="${sample_info}"
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46
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47 BARCODES="${barcodes}"
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48 LABELS="${labels}"
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49 METADATA="${metadata}"
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50 </configfile>
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51 </configfiles>
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52 <!-- The contents of the help tag is parsed as reStructuredText. Please see
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53 help-template.rst for examples of commonly-used sections in other Galaxy
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54 tools. -->
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55 <help>
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56
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57 .. class:: infomark
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58
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59 **What it does**
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60
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61 This tool parses sample information and creates a mapping of samples to
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62 barcodes. The sample information file must contain the columns ``sampleid``,
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63 ``barcode``, and ``reverse``, and can optionally contain a ``zone`` column
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64 also.
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65
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66 </help>
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67 </tool>
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