Mercurial > repos > peterjc > seq_select_by_id
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 |
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date | Thu, 11 May 2017 06:26:05 -0400 |
parents | 91f55ee8fea5 |
children | 8e1a90917fa7 |
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6:91f55ee8fea5 | 7:a5602454b0ad |
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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 |