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annotate bundle_collection.xml @ 1:cd6da887a5f4 draft

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author nml
date Fri, 04 Aug 2017 12:04:09 -0400
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1 <tool id="bundle_collection" name="Bundle Collection" version="1.2.1">
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2 <description>Download a collection of files</description>
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3 <stdio>
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4 <exit_code range="1:" level="fatal" description="Unknown error has occurred"/>
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5 </stdio>
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6 <command interpreter="perl">bundle_collection.pl -h $html_file -p $html_file.files_path
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7
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8 #if $singles_or_list.type == "list":
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9
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10 #if $singles_or_list.input:
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11 #for $f in $singles_or_list.input.keys
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12 -i "$f,$singles_or_list.input[$f].ext=$singles_or_list.input[$f]"
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13 #if $singles_or_list.input[$f].metadata.bam_index and $singles_or_list.input[$f].metadata.bam_index != "None"
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14 #set $bamind = $f+","+$singles_or_list.input[$f].ext+".bai="+$singles_or_list.input[$f].metadata.bam_index
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15 -i "$bamind"
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16 #end if
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17 #end for
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18 #end if
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19 #elif $singles_or_list.type == "singles":
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20 #for $dataset in $singles_or_list.single_files
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21 #if $dataset.single_file:
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22 -i "$dataset.single_file.name,$dataset.single_file.ext=$dataset.single_file"
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23 #end if
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24
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25 #if $dataset.single_file.metadata.bam_index and $dataset.single_file.metadata.bam_index != "None"
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26 #set $bamind = $dataset.single_file.name+","+$dataset.single_file.ext+".bai="+$dataset.single_file.metadata.bam_index
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27 -i "$bamind"
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28 #end if
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29
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30 #end for
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31 #end if
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32 </command>
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33
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34 <inputs>
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35 <conditional name="singles_or_list">
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36 <param name="type" type="select" label="Bundle type">
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37 <option value="singles">Individual datasets</option>
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38 <option value="list">List Collection </option>
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39 </param>
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40 <when value="singles">
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41 <repeat name='single_files' title='Single dataset(s)'>
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42 <param name="single_file" label="Dataset to add the bundle" type="data" format='data' optional='False'/>
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43 </repeat>
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44 </when>
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45 <when value="list">
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46 <param name="input" type="data_collection" label="Data Collection" collection_type="list" optional='False'/>
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47 </when>
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48 </conditional>
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49 </inputs>
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50
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51 <outputs>
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52 <data name="html_file" format="html" label="Bundled Collection" />
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53 </outputs>
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54 <tests>
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55 <test>
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56 <output/>
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57 </test>
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58 </tests>
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59
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60 <help>
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61 ***What it does**
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62
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63 This tool will bundle up files in a list collection into a downloadable zip file
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64
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65 Author: Mariam Iskander and Jen Cabral
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66 </help>
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67
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68 <citations>
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69 </citations>
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70
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71 </tool>