tool output pattern syntax

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tool output pattern syntax


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

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