To partially answer my own question an good example is: bam merge https://testtoolshed.g2.bx.psu.edu/repository?repository_id=aa54716b697c872f...
The key parts are: <command> .... #for $input in $inputs .... <inputs> <param name="inputs" type="data" format="bam,sam" multiple="True" label="Files to merge" /> ...
One issue I still have is if there is information hidden in the input's name. Is there some way of passing this to the tool?
Christian ________________________________ From: galaxy-dev [galaxy-dev-bounces@lists.galaxyproject.org] on behalf of Christian Brenninkmeijer [christian.brenninkmeijer@manchester.ac.uk] Sent: Monday, January 11, 2016 2:05 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] tools to reduce list of datasets.
Hi All,
Can someone point me to documentations/ examples of how to write a tool to reduce a a list of datasets back into a single dataset.
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What I want to do is process multiple pairs of reads.
1. load all the fastq files.
2. create a list of pairs
3. Run tools of each pair in the list (As a seperate job for each pair)
4. Run a single tool over all the results of 3 at the same time! (One job which takes all the files/ whole collection) as input.
thanks in advance Christian