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annotate merge.xml @ 3:c0c988378838 draft

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planemo upload commit 6bde05f38465311441e89cfa070f03d3b6edad1b
author nml
date Mon, 24 Oct 2016 16:23:11 -0400
parents 4263967e8d40
children 25136a2b0cfe
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1 <tool id="collapse_dataset" name="Collapse Collection" version="3.0">
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2 <description>Collapse collection into single dataset in order of the collection</description>
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3 <command>
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4 <![CDATA[
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5
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6 (
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7 #for $f in $input_list#
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8 #if $filename.add_name:
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9 #if str($filename.place_name) == "same_once":
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10 printf "$f.element_identifier\t"; cat "$f";
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11 #elif str($filename.place_name) == "same_multiple":
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12 awk '{print "$f.element_identifier\t"$0}' "$f";
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13 #elif str($filename.place_name) == "above":
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14 printf "$f.element_identifier\n"; cat "$f";
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15 #end if
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16 #else:
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17 cat "$f" ;
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18 #end if
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19
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20 #end for#
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21 )
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22 > $output
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23
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24 ]]>
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25
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26 </command>
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27 <inputs>
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28 <param name="input_list" type="data" format="data" label="Collection of files to collapse into single dataset" help="" optional="false" multiple="true" />
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29 <conditional name="filename">
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30 <param name="add_name" type="boolean" display="checkboxes" label="Append File name"/>
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31 <when value="true">
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32 <param name="place_name" type="select" label="Where to add dataset name">
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33 <option value="same_once">Same line and only once per dataset</option>
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34 <option value="same_multiple">Same line and each line in dataset</option>
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35 <option value="above">Line Above</option>
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36 </param>
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37 </when>
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38 <when value='false'>
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39 </when>
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40 </conditional>
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41 </inputs>
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42 <outputs>
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43 <data name="output" format_source="input_list" ></data>
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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name="input_list">
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48 <collection type="list">
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49 <element name="input1" value="input1" />
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50 <element name="input2" value="input2" />
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51 </collection>
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52 </param>
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53 <output name="output" file="answer.txt"/>
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54 </test>
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55 </tests>
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56 <help>
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57 Combines a list collection into a single file dataset with option to include dataset names.
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58 </help>
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59 <citations>
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60 </citations>
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61 </tool>