Mercurial > repos > peterjc > blast_rbh
changeset 20:e8f8c580bcca draft
planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/blast_rbh commit 05c2a834609f1fd02372c4f9b0a0733680fe9675-dirty
| author | peterjc |
|---|---|
| date | Fri, 15 May 2015 05:47:40 -0400 |
| parents | b6531758b428 |
| children | b41f8c43705e |
| files | tools/blast_rbh/README.rst tools/blast_rbh/blast_rbh.xml |
| diffstat | 2 files changed, 38 insertions(+), 29 deletions(-) [+] |
line wrap: on
line diff
--- a/tools/blast_rbh/README.rst Tue Jan 27 05:26:30 2015 -0500 +++ b/tools/blast_rbh/README.rst Fri May 15 05:47:40 2015 -0400 @@ -1,7 +1,7 @@ Find BLAST Reciprocal Best Hits (RBH), with Galaxy wrapper ========================================================== -This tool is copyright 2011-2014 by Peter Cock, The James Hutton Institute +This tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. @@ -80,6 +80,8 @@ - Updated to depend on NCBI BLAST+ 2.2.30 via ToolShed install. v0.1.6 - Offer the new blastp-fast task added in BLAST+ 2.2.30. - Added "NCBI BLAST+ integrated into Galaxy" preprint citation. +v0.1.7 - Reorder XML elements (internal change only). + - Planemo for Tool Shed upload (``.shed.yml``, internal change only). ======= ====================================================================== @@ -89,31 +91,40 @@ This tool is developed on the following GitHub repository: https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I 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_upload --shed_target testtoolshed --check_diff ~/repositories/galaxy_blast/tools/blast_rbh/ + ... - $ tar -czf blast_rbh.tar.gz tools/blast_rbh/README.rst tools/blast_rbh/blast_rbh.xml tools/blast_rbh/blast_rbh.py tools/blast_rbh/tool_dependencies.xml test-data/rhodopsin_nucs.fasta test-data/rhodopsin_proteins.fasta test-data/three_human_mRNA.fasta test-data/four_human_proteins.fasta test-data/k12_edited_proteins.fasta test-data/k12_ten_proteins.fasta test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular test-data/rbh_none.tabular test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular test-data/rbh_blastp_k12.tabular test-data/rbh_blastp_k12_self.tabular +or:: + + $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/galaxy_blast/tools/blast_rbh/ + ... + +To just build and check the tar ball, use:: -Check this worked:: - - $ tar -tzf blast_rbh.tar.gz - tools/blast_rbh/README.rst - tools/blast_rbh/blast_rbh.xml - tools/blast_rbh/blast_rbh.py - tools/blast_rbh/tool_dependencies.xml + $ planemo shed_upload --tar_only ~/repositories/galaxy_blast/tools/blast_rbh/ + ... + $ tar -tzf shed_upload.tar.gz + test-data/four_human_proteins.fasta + test-data/k12_edited_proteins.fasta + test-data/k12_ten_proteins.fasta + test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular + test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular + test-data/rbh_blastp_k12.tabular + test-data/rbh_blastp_k12_self.tabular + test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular + test-data/rbh_none.tabular + test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular test-data/rhodopsin_nucs.fasta test-data/rhodopsin_proteins.fasta test-data/three_human_mRNA.fasta - test-data/four_human_proteins.fasta - test-data/k12_edited_proteins.fasta - test-data/k12_ten_proteins.fasta - test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular - test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular - test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular - test-data/rbh_none.tabular - test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular - test-data/rbh_blastp_k12.tabular - test-data/rbh_blastp_k12_self.tabular + tools/blast_rbh/README.rst + tools/blast_rbh/blast_rbh.py + tools/blast_rbh/blast_rbh.xml + tools/blast_rbh/tool_dependencies.xml Licence (MIT)
--- a/tools/blast_rbh/blast_rbh.xml Tue Jan 27 05:26:30 2015 -0500 +++ b/tools/blast_rbh/blast_rbh.xml Fri May 15 05:47:40 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.6"> +<tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.7"> <description>from two FASTA files</description> <requirements> <requirement type="package" version="1.64">biopython</requirement> @@ -8,6 +8,11 @@ <requirement type="binary">blastn</requirement> <requirement type="package" version="2.2.30">blast+</requirement> </requirements> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> <version_command interpreter="python"> blast_rbh.py --version </version_command> @@ -24,11 +29,6 @@ -c $q_cover -o "$output" </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> <inputs> <!-- Galaxy does not have sub-types for protein vs nucletide FASTA --> <param name="fasta_a" type="data" format="fasta" @@ -72,8 +72,6 @@ <outputs> <data name="output" format="tabular" label="BLAST RBH: $fasta_a.name vs $fasta_b.name" /> </outputs> - <requirements> - </requirements> <tests> <test> <param name="fasta_a" value="four_human_proteins.fasta" ftype="fasta"/>