Question: Can I keep "on data xx" when including label in output
0
gravatar for 18Kbeyond
6 weeks ago by
18Kbeyond20
New York
18Kbeyond20 wrote:

Hi. I feel it's very helpful to have "on data xx" in the output name, as the default output name displays. e.g. filer_file_on_data_1

Is there a way I can have "on data xx" when I include "label" option in output like below? mutationType is an input parameter which is a select list.

< data name="output" format="bed" label="${mutationType.value_label}" >

label output • 92 views
ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by 18Kbeyond20
0
gravatar for Jennifer Hillman Jackson
6 weeks ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

The variable ${input} is commonly the name of the input file if there is just one, but not always. When editing a workflow, the actual variable for a specific input file is given in the area where outputs can be renamed. Perhaps use that information to develop the script? This is included in each tool wrapper as well - the variables used to denote specific inputs.

So, the variables can vary. For example, MACS2 has two inputs: "input_treatment_file" and "input_control_file". Using ${input_treatment_file} in the new label will capture the dataset name associated with the "input_treatment_file". This can be combined with custom text to create a custom output dataset name.

Hope that helps! Jen, Galaxy team

ADD COMMENTlink written 6 weeks ago by Jennifer Hillman Jackson23k

Hi Jen, thank you. I might have made my question complicated. Please disregard the variable.

To put it simple, when I don't include the label option like below, the output file name will auto-include this nice feature "on data xx" in the end.

< data name="output" format="bed" >

possible output name: filter_on_data_xx (as the tool name is filter)

However, when I include the label option like below, the output file name will only be what I put after label.

< data name="output" format="bed" label="output_filter" >

Is there a way that I can still have "on data xx" when having label option?

i.e. output_filter_on_data_xx

ADD REPLYlink written 6 weeks ago by 18Kbeyond20

Maybe look at the tool you want to model after and see how the output file name is both described then written out?

Filter is in the tool shed here: https://toolshed.g2.bx.psu.edu/view/devteam/bamtools_filter/bd735cae4ce6

The tip files including the .xml can be reviewed directly there or at the git repo. This is the important part:

<outputs>
    <data format="txt" name="out_file2" label="${tool.name} on ${on_string}: JSON filter rules" />
    <data name="out_file1" format="bam" label="${tool.name} on ${on_string}: Filtered BAM" />
</outputs>

This is also described in the tool development docs here: https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-outputs-data

Hope that helps better - I was focused on workflow usage, not tool development in my original reply :/

ADD REPLYlink written 6 weeks ago by Jennifer Hillman Jackson23k

Thank you so much! on ${on_string} is exactly what I want.

ADD REPLYlink written 6 weeks ago by 18Kbeyond20

Great & sorry for misunderstanding the first time around!

ADD REPLYlink written 6 weeks ago by Jennifer Hillman Jackson23k
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