Mercurial > repos > peterjc > sample_seqs

comparison tools/sample_seqs/README.rst @ 4:d3aa9f25c24c draft

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v0.2.2 use format_source and other internal changes
author peterjc
date Wed, 05 Aug 2015 12:30:18 -0400
parents 02c13ef1a669
children 6b71ad5d43fb
comparison
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3:02c13ef1a669 4:d3aa9f25c24c
1 Galaxy tool to sub-sample sequence files 1 Galaxy tool to sub-sample sequence files
2 ======================================== 2 ========================================
3 3
4 This tool is copyright 2014-2014 by Peter Cock, The James Hutton Institute 4 This tool is copyright 2014-2015 by Peter Cock, The James Hutton Institute
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6 See the licence text below (MIT licence). 6 See the licence text below (MIT licence).
7 7
8 This tool is a short Python script (using Biopython library functions) 8 This tool is a short Python script (using Biopython library functions)
9 to sub-sample sequence files (in a range of formats including FASTA, FASTQ, 9 to sub-sample sequence files (in a range of formats including FASTA, FASTQ,
54 54
55 ======= ====================================================================== 55 ======= ======================================================================
56 Version Changes 56 Version Changes
57 ------- ---------------------------------------------------------------------- 57 ------- ----------------------------------------------------------------------
58 v0.0.1 - Initial version. 58 v0.0.1 - Initial version.
59 v0.1.1 - Using optparse to provide a proper command line API. 59 v0.1.1 - Using ``optparse`` to provide a proper Python command line API.
60 v0.1.2 - Interleaved mode for working with paired records. 60 v0.1.2 - Interleaved mode for working with paired records.
61 - Tool definition now embeds citation information. 61 - Tool definition now embeds citation information.
62 v0.2.0 - Option to give number of sequences (or pairs) desired. 62 v0.2.0 - Option to give number of sequences (or pairs) desired.
63 This works by first counting all your sequences, then calculates 63 This works by first counting all your sequences, then calculates
64 the percentage required in order to sample them uniformly (evenly). 64 the percentage required in order to sample them uniformly (evenly).
65 This makes two passes through the input and is therefore slower. 65 This makes two passes through the input and is therefore slower.
66 v0.2.1 - Was missing a file for the functional tests. 66 v0.2.1 - Was missing a file for the functional tests.
67 - Included testing of stdout messages. 67 - Included testing of stdout messages.
68 - Includes testing of failure modes. 68 - Includes testing of failure modes.
69 v0.2.2 - Reorder XML elements (internal change only).
70 - Use ``format_source=...``` tag.
71 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
69 ======= ====================================================================== 72 ======= ======================================================================
70 73
71 74
72 Developers 75 Developers
73 ========== 76 ==========
74 77
75 This script and related tools are being developed on this GitHub repository: 78 This script and related tools are being developed on this GitHub repository:
76 https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 79 https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs
77 80
78 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use 81 For pushing a release to the test or main "Galaxy Tool Shed", use the following
79 the following command from the Galaxy root folder:: 82 Planemo commands (which requires you have set your Tool Shed access details in
83 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
80 84
81 $ tar -czf sample_seqs.tar.gz tools/sample_seqs/README.rst tools/sample_seqs/sample_seqs.py tools/sample_seqs/sample_seqs.xml tools/sample_seqs/tool_dependencies.xml test-data/ecoli.fastq test-data/ecoli.sample_N100.fastq test-data/ecoli.pair_sample_N100.fastq test-data/ecoli.sample_C10.fastq test-data/get_orf_input.Suis_ORF.prot.fasta test-data/get_orf_input.Suis_ORF.prot.sample_N100.fasta test-data/get_orf_input.Suis_ORF.prot.pair_sample_N100.fasta test-data/get_orf_input.Suis_ORF.prot.sample_C10.fasta test-data/get_orf_input.Suis_ORF.prot.pair_sample_C10.fasta test-data/MID4_GLZRM4E04_rnd30_frclip.sff test-data/MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff test-data/MID4_GLZRM4E04_rnd30_frclip.sample_C1.sff 85 $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/sample_seqs/
86 ...
82 87
83 Check this worked:: 88 or::
84 89
85 $ tar -tzf sample_seqs.tar.gz 90 $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/sample_seqs/
91 ...
92
93 To just build and check the tar ball, use::
94
95 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/sample_seqs/
96 ...
97 $ tar -tzf shed_upload.tar.gz
98 test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff
99 test-data/MID4_GLZRM4E04_rnd30_frclip.sff
100 test-data/MID4_GLZRM4E04_rnd30_frclip.sample_C1.sff
101 test-data/MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff
102 test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff
103 test-data/ecoli.fastq
104 test-data/ecoli.pair_sample_N100.fastq
105 test-data/ecoli.sample_C10.fastq
106 test-data/ecoli.sample_N100.fastq
107 test-data/get_orf_input.Suis_ORF.prot.fasta
108 test-data/get_orf_input.Suis_ORF.prot.pair_sample_C10.fasta
109 test-data/get_orf_input.Suis_ORF.prot.pair_sample_N100.fasta
110 test-data/get_orf_input.Suis_ORF.prot.sample_C10.fasta
111 test-data/get_orf_input.Suis_ORF.prot.sample_N100.fasta
86 tools/sample_seqs/README.rst 112 tools/sample_seqs/README.rst
87 tools/sample_seqs/sample_seqs.py 113 tools/sample_seqs/sample_seqs.py
88 tools/sample_seqs/sample_seqs.xml 114 tools/sample_seqs/sample_seqs.xml
89 tools/sample_seqs/tool_dependencies.xml 115 tools/sample_seqs/tool_dependencies.xml
90 test-data/ecoli.fastq
91 test-data/ecoli.sample_N100.fastq
92 test-data/ecoli.pair_sample_N100.fastq
93 test-data/ecoli.sample_C10.fastq
94 test-data/get_orf_input.Suis_ORF.prot.fasta
95 test-data/get_orf_input.Suis_ORF.prot.sample_N100.fasta
96 test-data/get_orf_input.Suis_ORF.prot.pair_sample_N100.fasta
97 test-data/get_orf_input.Suis_ORF.prot.sample_C10.fasta
98 test-data/get_orf_input.Suis_ORF.prot.pair_sample_C10.fasta
99 test-data/MID4_GLZRM4E04_rnd30_frclip.sff
100 test-data/MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff
101 test-data/MID4_GLZRM4E04_rnd30_pair_sample.sff
102 test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff
103 test-data/MID4_GLZRM4E04_rnd30_frclip.sample_C1.sff
104 116
105 117
106 Licence (MIT) 118 Licence (MIT)
107 ============= 119 =============
108 120