Mercurial > repos > matthias > stacks2_refmap

comparison todo.txt @ 0:bd0bf17caa4d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 98327d2948ae1ccb5aef5db9ab88605fd74a0de7-dirty
author matthias
date Thu, 29 Nov 2018 11:38:05 -0500
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children 93fb82c0fc94
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-1:000000000000 0:bd0bf17caa4d
1 For new tools I tried to add sections analogous to the strcuture
2 of stacks help output. Since we break compatibility to the stacks 1.48
3 wrappers anyway we should think of doing this for the tools that were
4 present already in 1.48 as well. Furthermore stacks help does not categorize
5 the single letter options (-x,...), would be nice to put them in the correct
6 section / conditional as well.
7
8
9
10
11 Raw Reads
12 process_radtags planemo test-data-generated-wdefaults sufficient-test
13 process_shortreads
14 parameters
15 clone_filter
16 parameters
17 kmer_filter
18
19 Core
20
21 ustacks parameters planemo test-data-generated-wdefaults sufficient-test
22 cstacks parameters planemo test-data-generated-wdefaults sufficient-test
23 sstacks parameters planemo test-data-generated-wdefaults sufficient-test
24 tsv2bam parameters planemo test-data-generated-wdefaults sufficient-test
25 gstacks parameters planemo test-data-generated-wdefaults
26 populations parameters planemo test-data-generated-wdefaults
27
28 tools
29 tool
30
31 Execution control
32
33 denovo_map.pl
34 ref_map.pl
35
36 TODO
37 - tools that accept iput from multiple previous stacks tools need a condition
38 to separate: 1) separate inputs 2) input from pipeline output
39
40 alternatively let the user merge the collections
41
42 - change input description in fastq_input_macro using tools
43 - remove pipes (as in tsv2bam)
44 - make log output optional
45 - denovo should also unzip stacks_outputs/catalog.calls to get the vcf
46 - loops in procrad and ustacks should not use name only (multiple elements might have the same name)
47 - help updates
48 - test stacks_summary from bioconda