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comparison tools/sample_seqs/README.rst @ 2:da64f6a9e32b draft

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Uploaded v0.2.0, adds desired count mode
author peterjc
date Fri, 06 Mar 2015 11:48:09 -0500
parents 16ecf25d521f
children 02c13ef1a669
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1:16ecf25d521f 2:da64f6a9e32b
37 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the 37 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
38 tool. One suggested location is in the filters section. Simply add the line:: 38 tool. One suggested location is in the filters section. Simply add the line::
39 39
40 <tool file="sample_seqs/sample_seqs.xml" /> 40 <tool file="sample_seqs/sample_seqs.xml" />
41 41
42 You will also need to install Biopython 1.62 or later. If you want to run 42 You will also need to install Biopython 1.62 or later.
43 the unit tests, include this line in ``tools_conf.xml.sample`` and the sample
44 FASTA files under the ``test-data`` directory. Then::
45 43
46 ./run_functional_tests.sh -id sample_seqs 44 If you wish to run the unit tests, also move/copy the ``test-data/`` files
45 under Galaxy's ``test-data/`` folder. Then::
46
47 ./run_tests.sh -id sample_seqs
47 48
48 That's it. 49 That's it.
49 50
50 51
51 History 52 History
53 54
54 ======= ====================================================================== 55 ======= ======================================================================
55 Version Changes 56 Version Changes
56 ------- ---------------------------------------------------------------------- 57 ------- ----------------------------------------------------------------------
57 v0.0.1 - Initial version. 58 v0.0.1 - Initial version.
59 v0.1.1 - Using optparse to provide a proper command line API.
60 v0.1.2 - Interleaved mode for working with paired records.
61 - Tool definition now embeds citation information.
62 v0.2.0 - Option to give number of sequences (or pairs) desired.
63 This works by first counting all your sequences, then calculates
64 the percentage required in order to sample them uniformly (evenly).
65 This makes two passes through the input and is therefore slower.
58 ======= ====================================================================== 66 ======= ======================================================================
59 67
60 68
61 Developers 69 Developers
62 ========== 70 ==========
65 https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs 73 https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs
66 74
67 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use 75 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
68 the following command from the Galaxy root folder:: 76 the following command from the Galaxy root folder::
69 77
70 $ 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/get_orf_input.Suis_ORF.prot.fasta test-data/get_orf_input.Suis_ORF.prot.sample_N100.fasta test-data/MID4_GLZRM4E04_rnd30_frclip.sff test-data/MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff 78 $ 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
71 79
72 Check this worked:: 80 Check this worked::
73 81
74 $ tar -tzf sample_seqs.tar.gz 82 $ tar -tzf sample_seqs.tar.gz
75 tools/sample_seqs/README.rst 83 tools/sample_seqs/README.rst
76 tools/sample_seqs/sample_seqs.py 84 tools/sample_seqs/sample_seqs.py
77 tools/sample_seqs/sample_seqs.xml 85 tools/sample_seqs/sample_seqs.xml
78 tools/sample_seqs/tool_dependencies.xml 86 tools/sample_seqs/tool_dependencies.xml
79 test-data/ecoli.fastq 87 test-data/ecoli.fastq
80 test-data/ecoli.sample_N100.fastq 88 test-data/ecoli.sample_N100.fastq
89 test-data/ecoli.pair_sample_N100.fastq
90 test-data/ecoli.sample_C10.fastq
81 test-data/get_orf_input.Suis_ORF.prot.fasta 91 test-data/get_orf_input.Suis_ORF.prot.fasta
82 test-data/get_orf_input.Suis_ORF.prot.sample_N100.fasta 92 test-data/get_orf_input.Suis_ORF.prot.sample_N100.fasta
93 test-data/get_orf_input.Suis_ORF.prot.pair_sample_N100.fasta
94 test-data/get_orf_input.Suis_ORF.prot.sample_C10.fasta
95 test-data/get_orf_input.Suis_ORF.prot.pair_sample_C10.fasta
83 test-data/MID4_GLZRM4E04_rnd30_frclip.sff 96 test-data/MID4_GLZRM4E04_rnd30_frclip.sff
84 test-data/MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff 97 test-data/MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff
98 test-data/MID4_GLZRM4E04_rnd30_pair_sample.sff
99 test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff
100 test-data/MID4_GLZRM4E04_rnd30_frclip.sample_C1.sff
85 101
86 102
87 Licence (MIT) 103 Licence (MIT)
88 ============= 104 =============
89 105