| Previous changeset 3:02c13ef1a669 (2015-03-27) Next changeset 5:6b71ad5d43fb (2017-02-01) |
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Commit message:
v0.2.2 use format_source and other internal changes |
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modified:
tools/sample_seqs/README.rst tools/sample_seqs/sample_seqs.xml |
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| diff -r 02c13ef1a669 -r d3aa9f25c24c tools/sample_seqs/README.rst --- a/tools/sample_seqs/README.rst Fri Mar 27 09:34:27 2015 -0400 +++ b/tools/sample_seqs/README.rst Wed Aug 05 12:30:18 2015 -0400 |
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| @@ -1,7 +1,7 @@ Galaxy tool to sub-sample sequence files ======================================== -This tool is copyright 2014-2014 by Peter Cock, The James Hutton Institute +This tool is copyright 2014-2015 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below (MIT licence). @@ -56,7 +56,7 @@ Version Changes ------- ---------------------------------------------------------------------- v0.0.1 - Initial version. -v0.1.1 - Using optparse to provide a proper command line API. +v0.1.1 - Using ``optparse`` to provide a proper Python command line API. v0.1.2 - Interleaved mode for working with paired records. - Tool definition now embeds citation information. v0.2.0 - Option to give number of sequences (or pairs) desired. @@ -66,6 +66,9 @@ v0.2.1 - Was missing a file for the functional tests. - Included testing of stdout messages. - Includes testing of failure modes. +v0.2.2 - Reorder XML elements (internal change only). + - Use ``format_source=...``` tag. + - Planemo for Tool Shed upload (``.shed.yml``, internal change only). ======= ====================================================================== @@ -75,32 +78,41 @@ This script and related tools are being developed on this GitHub repository: https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use -the following command from the Galaxy root folder:: +For pushing a release to the test or main "Galaxy Tool Shed", use the following +Planemo commands (which requires you have set your Tool Shed access details in +``~/.planemo.yml`` and that you have access rights on the Tool Shed):: + + $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/sample_seqs/ + ... + +or:: + + $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/sample_seqs/ + ... + +To just build and check the tar ball, use:: - $ 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 - -Check this worked:: - - $ tar -tzf sample_seqs.tar.gz + $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/sample_seqs/ + ... + $ tar -tzf shed_upload.tar.gz + test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff + test-data/MID4_GLZRM4E04_rnd30_frclip.sff + test-data/MID4_GLZRM4E04_rnd30_frclip.sample_C1.sff + test-data/MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff + test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff + test-data/ecoli.fastq + test-data/ecoli.pair_sample_N100.fastq + test-data/ecoli.sample_C10.fastq + test-data/ecoli.sample_N100.fastq + test-data/get_orf_input.Suis_ORF.prot.fasta + test-data/get_orf_input.Suis_ORF.prot.pair_sample_C10.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.sample_N100.fasta 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_pair_sample.sff - test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff - test-data/MID4_GLZRM4E04_rnd30_frclip.sample_C1.sff Licence (MIT) |
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| diff -r 02c13ef1a669 -r d3aa9f25c24c tools/sample_seqs/sample_seqs.xml --- a/tools/sample_seqs/sample_seqs.xml Fri Mar 27 09:34:27 2015 -0400 +++ b/tools/sample_seqs/sample_seqs.xml Wed Aug 05 12:30:18 2015 -0400 |
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| @@ -1,9 +1,14 @@ -<tool id="sample_seqs" name="Sub-sample sequences files" version="0.2.1"> +<tool id="sample_seqs" name="Sub-sample sequences files" version="0.2.2"> <description>e.g. to reduce coverage</description> <requirements> <requirement type="package" version="1.65">biopython</requirement> <requirement type="python-module">Bio</requirement> </requirements> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> <version_command interpreter="python">sample_seqs.py --version</version_command> <command interpreter="python"> sample_seqs.py -f "$input_file.ext" -i "$input_file" -o "$output_file" @@ -18,11 +23,6 @@ --interleaved #end if </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> <inputs> <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file" help="FASTA, FASTQ, or SFF format." /> <conditional name="sampling"> @@ -45,7 +45,7 @@ <param name="interleaved" type="boolean" label="Interleaved paired reads" help="This mode keeps paired reads together (e.g. take every 5th read pair)" /> </inputs> <outputs> - <data name="output_file" format="input" metadata_source="input_file" label="${input_file.name} (sub-sampled)"/> + <data name="output_file" format_source="input_file" metadata_source="input_file" label="${input_file.name} (sub-sampled)"/> </outputs> <tests> <test> |