Another tool-related question, if I may:
I want to pass a string to a tool, and this string may contains CR/LF,
double quotes, Dollar signs, etc.
The simple XML looks like this:
<command interpreter="sh">my_tool.sh '$input > $output
<param type="text" name="input" area="true"
However, when I enter non alpha numeric characters, they are converted
to X (the actual character 'X') before being sent to my script.
double quotes are converted to "__dq__" and single quotes are converted
Is there a way to pass the string intact to my program ?
(Let's assume for now that I'm well aware of the security problems in
allowing a string to be passed on to a shell script...)
Greg Von Kuster wrote, On 08/18/2008 08:17 AM:
In your tool config, add the "metadata_source" attribute to the
<outputs> tag set, something like the following.
<data format="input" name="output"
Assaf Gordon wrote:
> I'm writing a tool which accepts interval files and output interval
> The input file has the metadata set (chr/start/end columns).
> How can I copy the metadata to the generated output file?
> Currently, the output file's metadata is always set to chrom=1,
> start=2, end=3 (which I guess is the default for BED format).
> Other galaxy tools do it, so I'm sure it's possible. Which python code
> is responsible for that (to be included in my tool's XML) ?
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