comparison tools/seq_select_by_id/README.rst @ 7:a5602454b0ad draft

v0.0.12 Depends on Biopython 1.67 via legacy Tool Shed package or bioconda; Python 3 compatible print function
author peterjc
date Thu, 11 May 2017 06:26:05 -0400
parents 91f55ee8fea5
children 8e1a90917fa7
comparison
equal deleted inserted replaced
6:91f55ee8fea5 7:a5602454b0ad
1 Galaxy tool to select FASTA, QUAL, FASTQ or SFF sequences by ID 1 Galaxy tool to select FASTA, QUAL, FASTQ or SFF sequences by ID
2 =============================================================== 2 ===============================================================
3 3
4 This tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute 4 This tool is copyright 2011-2017 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. 6 See the licence text below.
7 7
8 This tool is a short Python script (using Biopython library functions) to extract 8 This tool is a short Python script (using Biopython library functions) to extract
9 sequences from a FASTA, QUAL, FASTQ, or SFF file based on the list of IDs given 9 sequences from a FASTA, QUAL, FASTQ, or SFF file based on the list of IDs given
83 - Includes testing of failure modes. 83 - Includes testing of failure modes.
84 v0.0.11 - Use the ``format_source=...`` tag. 84 v0.0.11 - Use the ``format_source=...`` tag.
85 - Reorder XML elements (internal change only). 85 - Reorder XML elements (internal change only).
86 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). 86 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
87 - Quote filenames in case of spaces (internal change only). 87 - Quote filenames in case of spaces (internal change only).
88 v0.0.12 - Python style changes (internal change only).
89 - Use ``<command detect_errors="aggressive">`` (internal change only).
90 - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda.
91 - Python 3 compatible print function.
88 ======= ====================================================================== 92 ======= ======================================================================
89 93
90 94
91 Developers 95 Developers
92 ========== 96 ==========
99 103
100 For pushing a release to the test or main "Galaxy Tool Shed", use the following 104 For pushing a release to the test or main "Galaxy Tool Shed", use the following
101 Planemo commands (which requires you have set your Tool Shed access details in 105 Planemo commands (which requires you have set your Tool Shed access details in
102 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: 106 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
103 107
104 $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/seq_select_by_id/ 108 $ planemo shed_update -t testtoolshed --check_diff tools/seq_select_by_id/
105 ... 109 ...
106 110
107 or:: 111 or::
108 112
109 $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/seq_select_by_id/ 113 $ planemo shed_update -t toolshed --check_diff tools/seq_select_by_id/
110 ... 114 ...
111 115
112 To just build and check the tar ball, use:: 116 To just build and check the tar ball, use::
113 117
114 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/seq_select_by_id/ 118 $ planemo shed_upload --tar_only tools/seq_select_by_id/
115 ... 119 ...
116 $ tar -tzf shed_upload.tar.gz 120 $ tar -tzf shed_upload.tar.gz
117 test-data/k12_hypothetical.fasta 121 test-data/k12_hypothetical.fasta
118 test-data/k12_hypothetical.tabular 122 test-data/k12_hypothetical.tabular
119 test-data/k12_hypothetical_alt.tabular 123 test-data/k12_hypothetical_alt.tabular