Question: Retrieve Current History Name in XML as variable
0
gravatar for dgygax
4.3 years ago by
dgygax • 50
United States
dgygax • 50 wrote:

Hi,

Is there any way to retrieve the current history name in the XML file of a tool in galaxy. Within the tools folder I have a XML file that calls a python script to write reports. This tool writes a series of reports for each sample in a specified Set. Right now I specify the Set using the following:

    <inputs>

        <param name="Set_ID" size="20" type="text" label="Set ID" value="Enter Set"/>

    </inputs>

In this case the user has to type in the Set they want to work on. I do not want this as it could lead to errors.

Alternatively the current history is exactly the Set name. If I could enter something such as:

    <inputs>

        <param name="Set_ID"  type="hidden" value="$__current_history_name"/>

    </inputs>

Where $__current_history__name equals the name of the current history that would be great. I know that galaxy has other reserved variable such as $__user_email__ for the users email address. So my question is, is there a reserved variable for the current history, or any other way to access the current history name in the XML file for a tool?

galaxy xml tool • 1.2k views
ADD COMMENT • link • modified 4.3 years ago by jmchilton ♦ 1.1k • written 4.3 years ago by dgygax • 50
1
gravatar for Bjoern Gruening
4.3 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi,

sorry I have no concrete answer for you (also I'm not aware of such a function), but I wanted to point you to a great report tool from Saskia Hiltemann. Have a look at:

https://wiki.galaxyproject.org/Events/GCC2014/Abstracts/Talks#iReport:_HTML_Reporting_in_Galaxy

It's available in the Galaxy Tool Shed.

Bjoern

 

 

ADD COMMENT • link written 4.3 years ago by Bjoern Gruening ♦ 5.1k

Thanks, I will look at the tool.

ADD REPLY • link written 4.3 years ago by dgygax • 50
1
gravatar for jmchilton
4.3 years ago by
jmchilton ♦ 1.1k
United States
jmchilton ♦ 1.1k wrote:

I can confirm that there is no such variable. I have created a Trello card for this feature if you wish to vote for it - https://trello.com/c/HgO7bqgk.

Update: Opened pull request with this functionality here -https://bitbucket.org/galaxy/galaxy-central/pull-request/473/allow-tools-to-access-__history_name__/diff.

ADD COMMENT • link modified 4.3 years ago • written 4.3 years ago by jmchilton ♦ 1.1k

Thanks, I just voted. I believe this feature would be very helpful for some tools.

ADD REPLY • link written 4.3 years ago by dgygax • 50

As a follow up on this - the PR was rejected but I did discover an alternative way to obtain the history name. See .

ADD REPLY • link written 3.6 years ago by jmchilton ♦ 1.1k
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