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1 <tool id="hadoop_galaxy_cat_paths" name="Cat paths" version="0.1.0">
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2 <description>Concatenate all components of a pathset into a single file.</description>
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3 <requirements>
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4 <requirement type="package" version="0.11">pydoop</requirement>
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5 <requirement type="package" version="0.1.1">hadoop-galaxy</requirement>
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6 </requirements>
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7
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8 <command>
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9 #if $use_hadoop
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10 dist_cat_paths
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11 #else
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12 cat_paths
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13 #end if
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14 #if $delete_source
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15 --delete-source
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16 #end if
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17 $input_pathset $output_path
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18 </command>
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19
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20 <inputs>
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21 <param name="input_pathset" type="data" format="pathset" label="Input pathset">
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22 <validator type="empty_field" />
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23 </param>
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24 <param name="delete_source" type="boolean" checked="false" label="Delete remote input data"
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25 help="This option makes the tool move the data rather than copy it" />
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26 <param name="use_hadoop" type="boolean" checked="false" label="Use Hadoop-based program"
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27 help="The Galaxy workspace must be accessible by the Hadoop cluster (see help for details)" />
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28 </inputs>
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29
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30 <outputs>
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31 <!-- TODO: can we read the format from input pathset and transfer it to output? -->
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32 <data name="output_path" format="data" label="Concatenated dataset $input_pathset.name" />
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33 </outputs>
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34
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35 <stdio>
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36 <exit_code range="1:" level="fatal" />
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37 </stdio>
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38
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39 <help>
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40 Datasets represented as pathsets can be split in a number of files.
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41 This tool takes all of them and concatenates them into a single output file.
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42
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43 In your workflow, you'll need to explicitly set the appropriate data format on the
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44 output dataset with an Action to "Change Datatype".
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45
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46 "Delete remote input data" option
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47 ====================================
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48 With this option, after the data has been concated into the new Galaxy dataset,
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49 the original files that were referenced by the pathset are deleted. This effectively
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50 tells the action to "move" the data instead of a "copying" it and helps
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51 avoid amassing intermediate data in your Hadoop workspace.
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52
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53
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54 "Use Hadoop-based program" option
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55 ====================================
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56
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57 With this option you will use your entire Hadoop cluster to simultaneously write
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58 multiple parts of the final file. For this to be possible, the Hadoop nodes
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59 must be able to access the Galaxy file space directly. In addition, to achieve
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60 reasonable results the Galaxy workspace should on a parallel shared file system.
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61 </help>
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62 </tool>
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