Mercurial > repos > mvdbeek > symlink_files
comparison symlink_files.xml @ 0:909a7e8e9b30 draft
planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
| author | mvdbeek |
|---|---|
| date | Tue, 29 Nov 2016 10:03:30 -0500 |
| parents | |
| children | 46dc0dbd9f04 |
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| -1:000000000000 | 0:909a7e8e9b30 |
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| 1 <tool id="symlink_files" name="Symlink Files" version="0.1.3"> | |
| 2 <requirements> | |
| 3 </requirements> | |
| 4 <stdio> | |
| 5 <exit_code range="1:" /> | |
| 6 </stdio> | |
| 7 <command><![CDATA[ | |
| 8 #if $__user_email__ not in $__admin_users__: | |
| 9 exit 1 | |
| 10 #end if | |
| 11 | |
| 12 #if $input: | |
| 13 mkdir -p '$output_path' && | |
| 14 #if '$input.ext': | |
| 15 ln -fs '$input' '$output_path'/'$input.element_identifier'.'$input.ext' | |
| 16 #else: | |
| 17 ln -fs '$input' '$output_path'/'$input.element_identifier' | |
| 18 #end if | |
| 19 #end if | |
| 20 #if $input_collection: | |
| 21 mkdir -p '$output_path'/'$input_collection.name' && | |
| 22 #for $element in $input_collection: | |
| 23 ln -fs '$element' '$output_path'/'$input_collection.name'/'$element.element_identifier'.'$element.ext'; | |
| 24 #end for | |
| 25 #end if | |
| 26 #if $input_collection_paired: | |
| 27 mkdir -p '$output_path'/'$input_collection_paired.name' && | |
| 28 #for $element in $input_collection_paired: | |
| 29 ln -fs '$element.forward' '$output_path'/'$input_collection_paired.name'/'$element.element_identifier'-forward.'$element.ext'; | |
| 30 ln -fs '$element.reverse' '$output_path'/'$input_collection_paired.name'/'$element.element_identifier'-reverse.'$element.ext'; | |
| 31 #end for | |
| 32 #end if | |
| 33 #if $input_collection_list_paired: | |
| 34 #for $sample in $input_collection_list_paired: | |
| 35 mkdir -p '$output_path'/'$input_collection_list_paired.name' && | |
| 36 #for $element in $sample: | |
| 37 ln -fs '$element' '$output_path'/'$input_collection_list_paired.name'/'$sample.name'-$element.element_identifier.'$element.ext'; | |
| 38 #end for | |
| 39 #end for | |
| 40 #end if | |
| 41 ]]></command> | |
| 42 <inputs> | |
| 43 <param name="input" optional="true" type="data" help="The file you would like to export"/> | |
| 44 <param name="input_collection" optional="true" type="data_collection" collection_type="list" help="The collection you would like to export"/> | |
| 45 <param name="input_collection_paired" optional="true" type="data_collection" collection_type="paired" help="The collection you would like to export"/> | |
| 46 <param name="input_collection_list_paired" optional="true" type="data_collection" collection_type="list:paired" help="The collection you would like to export"/> | |
| 47 <param name="output_path" type="text" help="Path to export to"/> | |
| 48 </inputs> | |
| 49 <outputs> | |
| 50 </outputs> | |
| 51 <help><![CDATA[ | |
| 52 Creates symlinks to specified path. | |
| 53 ]]></help> | |
| 54 </tool> |