tool output pattern syntax

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view

tool output pattern syntax

Jochen Bick

I have a problem with the output of rcorrector which I would like to
wrap. The input are single-end or paired-end fastq file/s and the output
is the name (name of the input file) of the files plus ".cor.fq" so for

input: sample_R1.fastq, sample_R2.fastq

output: sample_R1.cor.fq, sample_R2.cor.fq

How can I catch the output?  something like:

<data name="output1" format="fastq" label="${} on ${on_string}:
             <discover_datasets pattern="$input1\_cor"/>

<data name="output2" format="fastq" label="${} on ${on_string}:
             <discover_datasets pattern="$input2\_cor"/>
             <filter>library['lib'] == 'paired'</filter>

but $input is the complete path ...

Has anyone an idea?

Cheer Jochen

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:

To search Galaxy mailing lists use the unified search at: