Question about expression in Galaxy tools
Hello everyone, I found regular expression could be available in the tool (filter and sort) ->Filter. I wonder whether it could be the same in the tool (Text Manipulation) ->Compute. I have checked that the fuction "len(c4.split('_'))" would return error. So, could anyone tell me if it was possible like this? The file A: chr1 10 40 NM_1234_exon_1 chr2 50 70 NM_1234_exon_2 Change the file A to the file B such as: chr1 10 40 NM_1234 chr2 50 70 NM_1234 May it is useless in the example. But the way could solve problems I met.
Hello, There are some tools in the group 'Text Manipulation' that do this sort of manipulation directly. Combined, many basic "unix" functions can be performed. Combine them to create custom tools using Workflows - even place them in your tool menu for seamless access. To move from file A to file B, use tools such as these as a rough example: * Convert delimiters to TAB (convert all "_" to tabs) * Add column to an existing dataset (could include a single "_" char, to be merged later) * Cut columns from a table (can be used to rearrange and leave behind unwanted columns) * Merge Columns together (merge the new "_" back where you want it) Compute and Select have some character filters on them for security reasons. If you were running your own Galaxy and it wasn't public, these could be removed of course. Also, a tool from the Tool Shed such as the 'Tool factory' could be used to turn pretty much any custom unix/shell (or other!) script that acts on text data into a full fledged, single tool - the tool that creates tools! That new tool could even be for a publicly hosted server use if you wanted to do that (I'd recommend a security test first though, as with any new tool!). And don't leave Tool Factory active on a public server - bad things could happen. I am positive others have come up with many more solutions in all sorts of flavors. Discussions like this are good for the galaxy-dev@bx.psu.edu mailing list if you are interested in interacting with the development community. More about the list is here, about joining, posting, and following along: http://wiki.galaxyproject.org/Support#Mailing_Lists Thanks! Jen Galaxy team On 8/29/13 9:38 AM, 师云 wrote:
Hello everyone, I found regular expression could be available in the tool (filter and sort) ->Filter. I wonder whether it could be the same in the tool (Text Manipulation) ->Compute. I have checked that the fuction "len(c4.split('_'))" would return error. So, could anyone tell me if it was possible like this? The file A: chr1 10 40 NM_1234_exon_1 chr2 50 70 NM_1234_exon_2 Change the file A to the file B such as: chr1 10 40 NM_1234 chr2 50 70 NM_1234 May it is useless in the example. But the way could solve problems I met.
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Hi Jen, Thank you for your help. The Galaxy tools can do many things! From: Jennifer Jackson Sent: Friday, August 30, 2013 8:31 AM To: 师云 Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Question about expression in Galaxy tools Hello, There are some tools in the group 'Text Manipulation' that do this sort of manipulation directly. Combined, many basic "unix" functions can be performed. Combine them to create custom tools using Workflows - even place them in your tool menu for seamless access. To move from file A to file B, use tools such as these as a rough example: * Convert delimiters to TAB (convert all "_" to tabs) * Add column to an existing dataset (could include a single "_" char, to be merged later) * Cut columns from a table (can be used to rearrange and leave behind unwanted columns) * Merge Columns together (merge the new "_" back where you want it) Compute and Select have some character filters on them for security reasons. If you were running your own Galaxy and it wasn't public, these could be removed of course. Also, a tool from the Tool Shed such as the 'Tool factory' could be used to turn pretty much any custom unix/shell (or other!) script that acts on text data into a full fledged, single tool - the tool that creates tools! That new tool could even be for a publicly hosted server use if you wanted to do that (I'd recommend a security test first though, as with any new tool!). And don't leave Tool Factory active on a public server - bad things could happen. I am positive others have come up with many more solutions in all sorts of flavors. Discussions like this are good for the galaxy-dev@bx.psu.edu mailing list if you are interested in interacting with the development community. More about the list is here, about joining, posting, and following along: http://wiki.galaxyproject.org/Support#Mailing_Lists Thanks! Jen Galaxy team On 8/29/13 9:38 AM, 师云 wrote: Hello everyone, I found regular expression could be available in the tool (filter and sort) ->Filter. I wonder whether it could be the same in the tool (Text Manipulation) ->Compute. I have checked that the fuction "len(c4.split('_'))" would return error. So, could anyone tell me if it was possible like this? The file A: chr1 10 40 NM_1234_exon_1 chr2 50 70 NM_1234_exon_2 Change the file A to the file B such as: chr1 10 40 NM_1234 chr2 50 70 NM_1234 May it is useless in the example. But the way could solve problems I met. ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org
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