Re: [galaxy-dev] tool data_column param issue under workflow mode
Hi If you load a tabular table with type auto there is a possibility that it incorrectly sniffed as a csv file. With type csv the columns are split on commas and not tabs so the data appears in one column. This is especially the case for tab separated files that do not have row names and therefore the same number of tabs in the header row as the next row. Manually change the type to tabular which will solve the problem. One possible solution which add a stricter csv sniff method is in: https://github.com/galaxyproject/galaxy/pull/1156 regards Christian University of Manchester ________________________________ From: Christian Brenninkmeijer Sent: Wednesday, November 25, 2015 9:23 AM To: FGiacomoni INRA Subject: RE: [galaxy-dev] tool data_column param issue under workflow mode Hi If you load a tabular table with type auto there is a possibility that it incorrectly sniffed as a csv file. With type csv the columns are split on commas and not tabs. This is especially the case for tab separated files that do not have row names and therefor the same number of tabs in the header row as the next row. Manually change the type to tabular which will solve the problem. One possible solution which add a stricter csv sniff is in: https://github.com/galaxyproject/galaxy/pull/1156 regards Christian ________________________________ From: galaxy-dev [galaxy-dev-bounces@lists.galaxyproject.org] on behalf of FGiacomoni INRA [franck.giacomoni@clermont.inra.fr] Sent: Tuesday, November 24, 2015 2:16 PM To: galaxy-dev@lists.galaxyproject.org Subject: [galaxy-dev] tool data_column param issue under workflow mode Dears, We observed this issue under galaxy release 15.07. Tools with a param tag and type="data_column" in their xml file are impossible to set on a workflow "run" mode. The value of the column stay at "column 1" or void even if your tabular file has more than one column. The setting of the tool is ok in the "analyze data" mode : you can change the value of the column. We tested this issue with home made tools but also with Merge Columns (version 1.0.1) tool - "text manipulation" section on our Galaxy instance. and we detected the issue on the galaxy main instance too... Any idea ? Thanks Marion & Franck
Hi! Same problem here but only if my workflow start with an "input type" tool or any other tool, i can not select an option in list for workflow's other tools cf: https://dl.dropboxusercontent.com/u/86878089/Screen%20Shot%202015-11-25%20at... definitely not a data type problem ^^' sincerely nils On 25 November 2015 at 10:30, Christian Brenninkmeijer < christian.brenninkmeijer@manchester.ac.uk> wrote:
Hi
If you load a tabular table with type auto there is a possibility that it incorrectly sniffed as a csv file. With type csv the columns are split on commas and not tabs so the data appears in one column.
This is especially the case for tab separated files that do not have row names and therefore the same number of tabs in the header row as the next row.
Manually change the type to tabular which will solve the problem.
One possible solution which add a stricter csv sniff method is in:
https://github.com/galaxyproject/galaxy/pull/1156
regards Christian University of Manchester ------------------------------ *From:* Christian Brenninkmeijer *Sent:* Wednesday, November 25, 2015 9:23 AM *To:* FGiacomoni INRA *Subject:* RE: [galaxy-dev] tool data_column param issue under workflow mode
Hi
If you load a tabular table with type auto there is a possibility that it incorrectly sniffed as a csv file. With type csv the columns are split on commas and not tabs.
This is especially the case for tab separated files that do not have row names and therefor the same number of tabs in the header row as the next row.
Manually change the type to tabular which will solve the problem.
One possible solution which add a stricter csv sniff is in:
https://github.com/galaxyproject/galaxy/pull/1156
regards Christian ------------------------------ *From:* galaxy-dev [galaxy-dev-bounces@lists.galaxyproject.org] on behalf of FGiacomoni INRA [franck.giacomoni@clermont.inra.fr] *Sent:* Tuesday, November 24, 2015 2:16 PM *To:* galaxy-dev@lists.galaxyproject.org *Subject:* [galaxy-dev] tool data_column param issue under workflow mode
Dears, We observed this issue under galaxy release 15.07. Tools with a param tag and type="data_column" in their xml file are impossible to set on a workflow "run" mode. The value of the column stay at "column 1" or void even if your tabular file has more than one column.
The setting of the tool is ok in the "analyze data" mode : you can change the value of the column.
We tested this issue with home made tools but also with Merge Columns (version 1.0.1) tool - "text manipulation" section on our Galaxy instance. and we detected the issue on the galaxy main instance too...
Any idea ? Thanks Marion & Franck
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Thx for reporting this. I am looking into it. On Wed, Nov 25, 2015 at 4:53 AM, Nils Paulhe <nils.paulhe@gmail.com> wrote:
Hi!
Same problem here but only if my workflow start with an "input type" tool or any other tool, i can not select an option in list for workflow's other tools cf: https://dl.dropboxusercontent.com/u/86878089/Screen%20Shot%202015-11-25%20at...
definitely not a data type problem ^^'
sincerely
nils
On 25 November 2015 at 10:30, Christian Brenninkmeijer < christian.brenninkmeijer@manchester.ac.uk> wrote:
Hi
If you load a tabular table with type auto there is a possibility that it incorrectly sniffed as a csv file. With type csv the columns are split on commas and not tabs so the data appears in one column.
This is especially the case for tab separated files that do not have row names and therefore the same number of tabs in the header row as the next row.
Manually change the type to tabular which will solve the problem.
One possible solution which add a stricter csv sniff method is in:
https://github.com/galaxyproject/galaxy/pull/1156
regards Christian University of Manchester ------------------------------ *From:* Christian Brenninkmeijer *Sent:* Wednesday, November 25, 2015 9:23 AM *To:* FGiacomoni INRA *Subject:* RE: [galaxy-dev] tool data_column param issue under workflow mode
Hi
If you load a tabular table with type auto there is a possibility that it incorrectly sniffed as a csv file. With type csv the columns are split on commas and not tabs.
This is especially the case for tab separated files that do not have row names and therefor the same number of tabs in the header row as the next row.
Manually change the type to tabular which will solve the problem.
One possible solution which add a stricter csv sniff is in:
https://github.com/galaxyproject/galaxy/pull/1156
regards Christian ------------------------------ *From:* galaxy-dev [galaxy-dev-bounces@lists.galaxyproject.org] on behalf of FGiacomoni INRA [franck.giacomoni@clermont.inra.fr] *Sent:* Tuesday, November 24, 2015 2:16 PM *To:* galaxy-dev@lists.galaxyproject.org *Subject:* [galaxy-dev] tool data_column param issue under workflow mode
Dears, We observed this issue under galaxy release 15.07. Tools with a param tag and type="data_column" in their xml file are impossible to set on a workflow "run" mode. The value of the column stay at "column 1" or void even if your tabular file has more than one column.
The setting of the tool is ok in the "analyze data" mode : you can change the value of the column.
We tested this issue with home made tools but also with Merge Columns (version 1.0.1) tool - "text manipulation" section on our Galaxy instance. and we detected the issue on the galaxy main instance too...
Any idea ? Thanks Marion & Franck
___________________________________________________________ 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: https://lists.galaxyproject.org/
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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (3)
-
Aysam Guerler -
Christian Brenninkmeijer -
Nils Paulhe