Mercurial > repos > crs4 > hadoop_galaxy
comparison cat_paths.xml @ 0:7698311d4466 draft
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| author | crs4 |
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| date | Fri, 30 May 2014 06:48:47 -0400 |
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| -1:000000000000 | 0:7698311d4466 |
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| 1 <tool id="hadoop_galaxy_cat_paths" name="Cat paths" version="0.1.0"> | |
| 2 <description>Concatenate all components of a pathset into a single file.</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.11">pydoop</requirement> | |
| 5 <requirement type="package" version="0.1.1">hadoop-galaxy</requirement> | |
| 6 </requirements> | |
| 7 | |
| 8 <command> | |
| 9 #if $use_hadoop | |
| 10 dist_cat_paths | |
| 11 #else | |
| 12 cat_paths | |
| 13 #end if | |
| 14 #if $delete_source | |
| 15 --delete-source | |
| 16 #end if | |
| 17 $input_pathset $output_path | |
| 18 </command> | |
| 19 | |
| 20 <inputs> | |
| 21 <param name="input_pathset" type="data" format="pathset" label="Input pathset"> | |
| 22 <validator type="empty_field" /> | |
| 23 </param> | |
| 24 <param name="delete_source" type="boolean" checked="false" label="Delete remote input data" | |
| 25 help="This option makes the tool move the data rather than copy it" /> | |
| 26 <param name="use_hadoop" type="boolean" checked="false" label="Use Hadoop-based program" | |
| 27 help="The Galaxy workspace must be accessible by the Hadoop cluster (see help for details)" /> | |
| 28 </inputs> | |
| 29 | |
| 30 <outputs> | |
| 31 <!-- TODO: can we read the format from input pathset and transfer it to output? --> | |
| 32 <data name="output_path" format="data" label="Concatenated dataset $input_pathset.name" /> | |
| 33 </outputs> | |
| 34 | |
| 35 <stdio> | |
| 36 <exit_code range="1:" level="fatal" /> | |
| 37 </stdio> | |
| 38 | |
| 39 <help> | |
| 40 Datasets represented as pathsets can be split in a number of files. | |
| 41 This tool takes all of them and concatenates them into a single output file. | |
| 42 | |
| 43 In your workflow, you'll need to explicitly set the appropriate data format on the | |
| 44 output dataset with an Action to "Change Datatype". | |
| 45 | |
| 46 "Delete remote input data" option | |
| 47 ==================================== | |
| 48 With this option, after the data has been concated into the new Galaxy dataset, | |
| 49 the original files that were referenced by the pathset are deleted. This effectively | |
| 50 tells the action to "move" the data instead of a "copying" it and helps | |
| 51 avoid amassing intermediate data in your Hadoop workspace. | |
| 52 | |
| 53 | |
| 54 "Use Hadoop-based program" option | |
| 55 ==================================== | |
| 56 | |
| 57 With this option you will use your entire Hadoop cluster to simultaneously write | |
| 58 multiple parts of the final file. For this to be possible, the Hadoop nodes | |
| 59 must be able to access the Galaxy file space directly. In addition, to achieve | |
| 60 reasonable results the Galaxy workspace should on a parallel shared file system. | |
| 61 </help> | |
| 62 </tool> |