Mercurial > repos > peterjc > seq_filter_by_mapping

comparison tools/seq_filter_by_mapping/README.rst @ 2:48e71dfd51b3 draft

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v0.0.5 Depend on Biopython 1.67 from Tool Shed or (Bio)conda
author peterjc
date Wed, 10 May 2017 13:16:44 -0400
parents 8ff0ac66f1a3
children 481b0a925e66
comparison
equal deleted inserted replaced
1:8ff0ac66f1a3 2:48e71dfd51b3
1 Galaxy tool to filter FASTA, FASTQ or SFF sequences by SAM/BAM mapping 1 Galaxy tool to filter FASTA, FASTQ or SFF sequences by SAM/BAM mapping
2 ====================================================================== 2 ======================================================================
3 3
4 This tool is copyright 2014-2015 by Peter Cock, The James Hutton Institute 4 This tool is copyright 2014-2017 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) which 8 This tool is a short Python script (using Biopython library functions) which
9 divides a FASTA, FASTQ, or SFF file in two, those sequences which do or do 9 divides a FASTA, FASTQ, or SFF file in two, those sequences which do or do
64 v0.0.2 - Fixed some error messages. 64 v0.0.2 - Fixed some error messages.
65 v0.0.3 - Report counts for FASTQ as done for FASTA and SFF files. 65 v0.0.3 - Report counts for FASTQ as done for FASTA and SFF files.
66 v0.0.4 - Use the ``format_source=...`` tag. 66 v0.0.4 - Use the ``format_source=...`` tag.
67 - Reorder XML elements (internal change only). 67 - Reorder XML elements (internal change only).
68 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). 68 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
69 v0.0.5 - Python script cleanups (internal change only).
70 - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda.
71 - Use ``<command detect_errors="aggressive">`` (internal change only).
72 - Single quote command line arguments (internal change only).
69 ======= ====================================================================== 73 ======= ======================================================================
70 74
71 75
72 Developers 76 Developers
73 ========== 77 ==========
80 84
81 For pushing a release to the test or main "Galaxy Tool Shed", use the following 85 For pushing a release to the test or main "Galaxy Tool Shed", use the following
82 Planemo commands (which requires you have set your Tool Shed access details in 86 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):: 87 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
84 88
85 $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/seq_filter_by_mapping/ 89 $ planemo shed_update -t testtoolshed --check_diff tools/seq_filter_by_mapping/
86 ... 90 ...
87 91
88 or:: 92 or::
89 93
90 $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/seq_filter_by_mapping/ 94 $ planemo shed_update -t toolshed --check_diff tools/seq_filter_by_mapping/
91 ... 95 ...
92 96
93 To just build and check the tar ball, use:: 97 To just build and check the tar ball, use::
94 98
95 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/seq_filter_by_mapping/ 99 $ planemo shed_upload --tar_only tools/seq_filter_by_mapping/
96 ... 100 ...
97 $ tar -tzf shed_upload.tar.gz 101 $ tar -tzf shed_upload.tar.gz
98 test-data/SRR639755_mito_pairs.fastq.gz 102 test-data/SRR639755_mito_pairs.fastq.gz
99 test-data/SRR639755_sample_by_coord.sam 103 test-data/SRR639755_sample_by_coord.sam
100 test-data/SRR639755_sample_lax.fastq 104 test-data/SRR639755_sample_lax.fastq