Is there a way yet to more easily determine name of inputs for renaming in workflows
Hi, In order to make Galaxy workflows even more useful, it is going to be important for data files to be renamed in a workflow. I know we can use the "#{input1 | base name}-BWA.sam" trick which is useful IF you know what the actual parameter name is in the XML file. There was some discussions some years ago (http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-September/011288.html) but it is is now very time consuming to figure out from the XML file what the name of the input parameter is you would like to use (and it is often very tricky, due to the fact that the name of the actual input parameter may actually change based on some selection in the UI…. I often had to resort to actually chaining the XML file to make the output something like: <data format="sam" name="output" label="#echo os.path.splitext ( str ( $paired.input1.name ).replace ( '_R1' , '' )) [ 0 ]#-bwa_#echo str ( $paired.sPaired ) #.sam”> But that is time consuming and does no longer work with the toolshed since an update of a tool is merely a brute force replacement of the previous version, no longer allowing me to have to change it once and let the updates work with on the changed version as was working brilliantly before all tools were moved out of the main branch and into the toolshed)… So, are there any plans to at least expose the Inputs (or the XML) during the workflow editing or something similar? Now I have to dig up the XML file every time I use a new tool, making the creation of workflow a tedious task... Regards, Thon [cid:enz_logo_2_newf03327] Thon deBoer Director of Software 3415 Colorado Ave. Room A255 Boulder, CO 80303 Cell: (650) 799-6839 tdeboer@enzymatics.com www.enzymatics.com Enzymatics Inc. Confidentiality Notice: This e-mail and any attachments are confidential, proprietary and or privileged information. It is intended only for the individual(s) to whom it is addressed, and may not be saved, copied, printed, disclosed or used by anyone other than the intended recipient(s). If you are not an intended recipient, please delete this e-mail immediately and notify the sender by e-mail.
Would something as simple as showing the input parameter name in a tooltip inside the workflow editor accomplish what you need? -- James Taylor On Fri, Dec 27, 2013 at 4:24 PM, Thon deBoer <TdeBoer@enzymatics.com> wrote:
Hi,
In order to make Galaxy workflows even more useful, it is going to be important for data files to be renamed in a workflow. I know we can use the "#{input1 | base name}-BWA.sam" trick which is useful IF you know what the actual parameter name is in the XML file.
There was some discussions some years ago ( http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-September/011288.html) but it is is now very time consuming to figure out from the XML file what the name of the input parameter is you would like to use (and it is often very tricky, due to the fact that the name of the actual input parameter may actually change based on some selection in the UI….
I often had to resort to actually chaining the XML file to make the output something like:
<data format="sam" name="output" label="#echo os.path.splitext ( str ( $ paired.input1.name ).replace ( '_R1' , '' )) [ 0 ]#-bwa_#echo str ( $paired.sPaired ) #.sam”>
But that is time consuming and does no longer work with the toolshed since an update of a tool is merely a brute force replacement of the previous version, no longer allowing me to have to change it once and let the updates work with on the changed version as was working brilliantly before all tools were moved out of the main branch and into the toolshed)…
So, are there any plans to at least expose the Inputs (or the XML) during the workflow editing or something similar? Now I have to dig up the XML file every time I use a new tool, making the creation of workflow a tedious task... Regards,
Thon
*Thon deBoer **Director of Software*
3415 Colorado Ave. Room A255 Boulder, CO 80303
Cell: (650) 799-6839
tdeboer@enzymatics.com www.enzymatics.com
*Enzymatics Inc. Confidentiality Notice:* This e-mail and any attachments are confidential, proprietary and or privileged information. It is intended only for the individual(s) to whom it is addressed, and may not be saved, copied, printed, disclosed or used by anyone other than the intended recipient(s). If you are not an intended recipient, please delete this e-mail immediately and notify the sender by e-mail.
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Absolutely! As long as I don’t need to open up the XML file in the toolshed tree… Regards, Thon On Dec 31, 2013, at 11:53 AM, James Taylor <james@jamestaylor.org<mailto:james@jamestaylor.org>> wrote: Would something as simple as showing the input parameter name in a tooltip inside the workflow editor accomplish what you need? -- James Taylor On Fri, Dec 27, 2013 at 4:24 PM, Thon deBoer <TdeBoer@enzymatics.com<mailto:TdeBoer@enzymatics.com>> wrote: Hi, In order to make Galaxy workflows even more useful, it is going to be important for data files to be renamed in a workflow. I know we can use the "#{input1 | base name}-BWA.sam" trick which is useful IF you know what the actual parameter name is in the XML file. There was some discussions some years ago (http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-September/011288.html) but it is is now very time consuming to figure out from the XML file what the name of the input parameter is you would like to use (and it is often very tricky, due to the fact that the name of the actual input parameter may actually change based on some selection in the UI…. I often had to resort to actually chaining the XML file to make the output something like: <data format="sam" name="output" label="#echo os.path.splitext ( str ( $paired.input1.name<http://paired.input1.name/> ).replace ( '_R1' , '' )) [ 0 ]#-bwa_#echo str ( $paired.sPaired ) #.sam”> But that is time consuming and does no longer work with the toolshed since an update of a tool is merely a brute force replacement of the previous version, no longer allowing me to have to change it once and let the updates work with on the changed version as was working brilliantly before all tools were moved out of the main branch and into the toolshed)… So, are there any plans to at least expose the Inputs (or the XML) during the workflow editing or something similar? Now I have to dig up the XML file every time I use a new tool, making the creation of workflow a tedious task... Regards, Thon <enz_logo_2_newf03327.jpeg> Thon deBoer Director of Software 3415 Colorado Ave. Room A255 Boulder, CO 80303 Cell: (650) 799-6839<tel:%28650%29%20799-6839> tdeboer@enzymatics.com<mailto:tdeboer@enzymatics.com> www.enzymatics.com<http://www.enzymatics.com/> Enzymatics Inc. Confidentiality Notice: This e-mail and any attachments are confidential, proprietary and or privileged information. It is intended only for the individual(s) to whom it is addressed, and may not be saved, copied, printed, disclosed or used by anyone other than the intended recipient(s). If you are not an intended recipient, please delete this e-mail immediately and notify the sender by e-mail. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. 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/
I have created a Trello card for this request here - https://trello.com/c/Fk1mcGnZ. -John On Thu, Jan 2, 2014 at 11:48 AM, Thon deBoer <TdeBoer@enzymatics.com> wrote:
Absolutely!
As long as I don’t need to open up the XML file in the toolshed tree…
Regards,
Thon
On Dec 31, 2013, at 11:53 AM, James Taylor <james@jamestaylor.org> wrote:
Would something as simple as showing the input parameter name in a tooltip inside the workflow editor accomplish what you need?
-- James Taylor
On Fri, Dec 27, 2013 at 4:24 PM, Thon deBoer <TdeBoer@enzymatics.com>wrote:
Hi,
In order to make Galaxy workflows even more useful, it is going to be important for data files to be renamed in a workflow. I know we can use the "#{input1 | base name}-BWA.sam" trick which is useful IF you know what the actual parameter name is in the XML file.
There was some discussions some years ago ( http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-September/011288.html) but it is is now very time consuming to figure out from the XML file what the name of the input parameter is you would like to use (and it is often very tricky, due to the fact that the name of the actual input parameter may actually change based on some selection in the UI….
I often had to resort to actually chaining the XML file to make the output something like:
<data format="sam" name="output" label="#echo os.path.splitext ( str ( $ paired.input1.name ).replace ( '_R1' , '' )) [ 0 ]#-bwa_#echo str ( $paired.sPaired ) #.sam”>
But that is time consuming and does no longer work with the toolshed since an update of a tool is merely a brute force replacement of the previous version, no longer allowing me to have to change it once and let the updates work with on the changed version as was working brilliantly before all tools were moved out of the main branch and into the toolshed)…
So, are there any plans to at least expose the Inputs (or the XML) during the workflow editing or something similar? Now I have to dig up the XML file every time I use a new tool, making the creation of workflow a tedious task... Regards,
Thon
<enz_logo_2_newf03327.jpeg>
*Thon deBoer **Director of Software*
3415 Colorado Ave. Room A255 Boulder, CO 80303
Cell: (650) 799-6839
tdeboer@enzymatics.com www.enzymatics.com *Enzymatics Inc. Confidentiality Notice:* This e-mail and any attachments are confidential, proprietary and or privileged information. It is intended only for the individual(s) to whom it is addressed, and may not be saved, copied, printed, disclosed or used by anyone other than the intended recipient(s). If you are not an intended recipient, please delete this e-mail immediately and notify the sender by e-mail.
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. 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/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. 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/
participants (3)
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James Taylor -
John Chilton -
Thon deBoer