Hello alls
how to change the output filename of an action so that it becomes prefix_input filename (where I decide which prefix I want to add) rather than "action on data 1". I do not see how to do it in the "new output name" option
Thanks for your help
jp
You should be able to use the syntax #{tool_input_name} to grab the input filename, and can combine this with other text, for something like "YourPrefix on #{tool_input_name}".
One helpful tip is that if you're seeing a blank where you expected an input name to be, it probably means the tool's input name doesn't actually match. For example, the input might be 'input' instead of 'input1', etc. In recent versions of galaxy, valid inputs will be displayed in the Rename Action box as a reference.
Thanks Dannon but this does not work for me, the output name is either blank if I use #{input_file_variable} or "{#input_file_variable}" if I use {#input_file_variable}. Lastly, it becomes "MyPrefix on" if I use the syntax MyPrefix on ${#input_file_variable}. In this last case a new box appears in my workflow page which says:
Workflow Parameters
I don't know what to do next ;-( Best jp
2014-08-20 13:24 GMT+02:00 Dannon Baker on Galaxy Biostar < notifications@biostars.org>:
It's definitely the former (#) syntax, as the $ syntax is for workflow parameters, which while they can be used in combination with the rename actions, aren't what you're looking for.
Let me test a few things here and get back to you.
Editing the original response, so others find this easier. Turns out I needed one more coffee before I responded above.
I'm desperate, it doesn't work. Here is exactly what I do:
in my workflow canvas for testing this I have an Input dataset tool box and a FASTQ to FASTA tool box.
Within this last tool box , I create a new output_file and enter #{FASTQ to FASTA_input_name} in the New output name as you suggest
When I run the workflow, the name is empty
Which FASTQ to FASTA converter are you using? Here are examples, using both. Note the difference between "input" and "input_file".
https://www.dropbox.com/s/lu77ne1mqpq2r4r/Screenshot%202014-08-20%2011.33.17.png
https://www.dropbox.com/s/d24cn977duq3fno/Screenshot%202014-08-20%2011.33.20.png
To sumarize:
in the New output name window of a particulaenter: prefix #{input_file} or prefix #{input} depending on the tool being used
If you have several successive tools in your workflow be sure to do that for each tool if you want to keep track of the name of your input dataset. You end up with something like this in my case after 8 tools (each new prefix is in italic) but at least you keep the info that it concerns the IonXpress 018_TOR-126 dataset
118: IonXpress_018_TOR-126.fastq
213: Groomer IonXpress_018_TOR-126.fastq
214: FASTQ to Tabular Groomer IonXpress_018_TOR-126.fastq
215: Sort FASTQ to Tabular Groomer IonXpress_018_TOR-126.fastq
216: Tabular to FASTQ Sort FASTQ to Tabular Groomer IonXpress_018_TOR-126.fastq
217: Groomer Tabular to FASTQ Sort FASTQ to Tabular Groomer IonXpress_018_TOR-126.fastq
218: Filter Groomer Tabular to FASTQ Sort FASTQ to Tabular Groomer IonXpress_018_TOR-126.fastq
219: FASTA Filter Groomer Tabular to FASTQ Sort FASTQ to Tabular Groomer IonXpress_018_TOR-126.fastq
220: 500K FASTA Filter Groomer Tabular to FASTQ Sort FASTQ to Tabular Groomer IonXpress_018_TOR-126.fastq
