view todo.txt @ 3:ead5013ec8e4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73

For new tools I tried to add sections analogous to the strcuture
of stacks help output. Since we break compatibility to the stacks 1.48
wrappers anyway we should think of doing this for the tools that were
present already in 1.48 as well. Furthermore stacks help does not categorize
the single letter options (-x,...), would be nice to put them in the correct
section / conditional as well.

Raw Reads
    process_radtags planemo test-data-generated-wdefaults sufficient-test
    process_shortreads
        parameters 
    clone_filter
        parameters
    kmer_filter
        
Core

    ustacks parameters planemo test-data-generated-wdefaults sufficient-test
    cstacks parameters planemo test-data-generated-wdefaults sufficient-test
    sstacks parameters planemo test-data-generated-wdefaults sufficient-test
    tsv2bam parameters planemo test-data-generated-wdefaults sufficient-test
    gstacks parameters planemo test-data-generated-wdefaults
populations parameters planemo test-data-generated-wdefaults

tools
    tool 

Execution control

    denovo_map.pl
    ref_map.pl

TODO
- tools that accept iput from multiple previous stacks tools need a condition
  to separate: 1) separate inputs 2) input from pipeline output
  
  alternatively let the user merge the collections

- change input description in fastq_input_macro using tools 
- remove pipes (as in tsv2bam)
- make log output optional
- denovo should also unzip stacks_outputs/catalog.calls to get the vcf
- loops in procrad and ustacks should not use name only (multiple elements might have the same name)
- help updates
- test stacks_summary from bioconda