diff tools/blast_rbh/README.rst @ 20:e8f8c580bcca draft

planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/blast_rbh commit 05c2a834609f1fd02372c4f9b0a0733680fe9675-dirty

--- 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)