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1 <tool id="imgt_concatenate" name="IMGT Concatenate" version="1.0">
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2 <description> </description>
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3 <command interpreter="bash">
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4 imgt_concatenate.sh $out_file
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1
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5 #if str( $with_id.with_id_selector ) == "true":
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6 #for $i, $f in enumerate($with_id.files)
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7 "$f.file"
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8 "$f.id"
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9 #end for
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10 #else
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11 #for $i, $f in enumerate($with_id.files)
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12 "$f.file"
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13 ""
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14 #end for
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15 #end if
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16 </command>
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17 <inputs>
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1
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18 <conditional name="with_id">
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19 <param name="with_id_selector" type="select" label="Add a file ID to the sequence ID">
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20 <option value="true">Add file ID to SequenceID to identify the origin file</option>
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21 <option value="false" selected="True">Keep SequenceID as is</option>
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22 </param>
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23 <when value='true'>
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24 <repeat name="files" title="Sample" min="2" default="2">
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5
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25 <param name="file" type="data" format="data" label="IMGT zip file" />
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1
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26 <param name="id" type="text" label="ID for dataset" size="25">
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27 <validator type="regex" message="Fill in an ID">.+</validator>
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28 </param>
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29 </repeat>
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30 </when>
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31 <when value='false'>
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32 <repeat name="files" title="Sample" min="2" default="2">
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5
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33 <param name="file" type="data" format="data" label="IMGT zip file" />
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1
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34 </repeat>
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35 </when>
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36 </conditional>
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37 <param name="label" type="text" label="A name for the new dataset" size="25">
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38 <validator type="regex" message="Fill in a name for the new dataset">.+</validator>
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39 </param>
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40 </inputs>
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41 <outputs>
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3
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42 <data format="data" name="out_file" label="${label}"/>
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43 </outputs>
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44 <help>
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45 Concatenate two or more IMGT files to create one new IMGT zip with all the sequences of the inputs.
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46
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47 </help>
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48
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49 </tool>
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