Mercurial > repos > peterjc > seq_rename

changeset 16:e279ed332c8e draft

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planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/seq_rename commit b6a4aa926554f2973b537999ff53478117975064
author peterjc
date Wed, 13 May 2015 06:38:43 -0400
parents ba3ec1b3e635
children 21d7e700fbd7
files tools/seq_rename/README.rst tools/seq_rename/seq_rename.py tools/seq_rename/seq_rename.xml
diffstat 3 files changed, 35 insertions(+), 23 deletions(-) [+]
line wrap: on
line diff
--- a/tools/seq_rename/README.rst	Thu Nov 27 08:20:54 2014 -0500
+++ b/tools/seq_rename/README.rst	Wed May 13 06:38:43 2015 -0400
@@ -1,7 +1,7 @@
 Galaxy tool to rename FASTA, QUAL, FASTQ or SFF sequences
 =========================================================
 
-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.
 
@@ -75,6 +75,9 @@
         - Tool definition now embeds citation information.
         - If white space is found in the requested tabular field then only
           the first word is used as the identifier (with a warning to stderr).
+v0.0.7  - Use the ``format_source=...`` tag.
+        - Reorder XML elements (internal change only).
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
 ======= ======================================================================
 
 
@@ -87,21 +90,30 @@
 Development has now moved to a dedicated GitHub repository:
 https://github.com/peterjc/pico_galaxy/tree/master/tools
 
-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_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/seq_rename/
+    ...
+
+or::
 
-    $ tar -czf seq_rename.tar.gz tools/seq_rename/README.rst tools/seq_rename/seq_rename.* tools/seq_rename/tool_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.rename.tabular test-data/four_human_proteins.rename.fasta
+    $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/seq_rename/
+    ...
+
+To just build and check the tar ball, use::
 
-Check this worked::
-
-    $ tar -tzf seq_rename.tar.gz
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/seq_rename/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
+    test-data/four_human_proteins.fasta
+    test-data/four_human_proteins.rename.fasta
+    test-data/four_human_proteins.rename.tabular
     tools/seq_rename/README.rst
     tools/seq_rename/seq_rename.py
     tools/seq_rename/seq_rename.xml
     tools/seq_rename/tool_dependencies.xml
-    test-data/four_human_proteins.fasta
-    test-data/four_human_proteins.rename.tabular
-    test-data/four_human_proteins.rename.fasta
 
 
 Licence (MIT)
--- a/tools/seq_rename/seq_rename.py	Thu Nov 27 08:20:54 2014 -0500
+++ b/tools/seq_rename/seq_rename.py	Wed May 13 06:38:43 2015 -0400
@@ -27,7 +27,7 @@
     print "v0.0.6"
     sys.exit(0)
 
-def stop_err(msg, err=1):
+def sys_exit(msg, err=1):
     sys.stderr.write(msg.rstrip() + "\n")
     sys.exit(err)
 
@@ -35,7 +35,7 @@
 try:
     tabular_file, old_col_arg, new_col_arg, in_file, seq_format, out_file = sys.argv[1:]
 except ValueError:
-    stop_err("Expected six arguments (tabular file, old col, new col, input file, format, output file), got %i:\n%s" % (len(sys.argv)-1, " ".join(sys.argv)))
+    sys_exit("Expected six arguments (tabular file, old col, new col, input file, format, output file), got %i:\n%s" % (len(sys.argv)-1, " ".join(sys.argv)))
 
 try:
     if old_col_arg.startswith("c"):
@@ -43,16 +43,16 @@
     else:
         old_column = int(old_col_arg)-1
 except ValueError:
-    stop_err("Expected column number, got %s" % old_col_arg)
+    sys_exit("Expected column number, got %s" % old_col_arg)
 try:
     if old_col_arg.startswith("c"):
         new_column = int(new_col_arg[1:])-1
     else:
         new_column = int(new_col_arg)-1
 except ValueError:
-    stop_err("Expected column number, got %s" % new_col_arg)
+    sys_exit("Expected column number, got %s" % new_col_arg)
 if old_column == new_column:
-    stop_err("Old and new column arguments are the same!")
+    sys_exit("Old and new column arguments are the same!")
 
 def parse_ids(tabular_file, old_col, new_col):
     """Read tabular file and record all specified ID mappings.
@@ -109,7 +109,7 @@
     try:
         from Bio.SeqIO.SffIO import SffIterator, SffWriter
     except ImportError:
-        stop_err("Requires Biopython 1.54 or later")
+        sys_exit("Requires Biopython 1.54 or later")
 
     try:
         from Bio.SeqIO.SffIO import ReadRocheXmlManifest
@@ -142,7 +142,7 @@
         writer = fastqWriter(open(out_file, "w"))
         marker = "@"
     else:
-        stop_err("Unsupported file type %r" % seq_format)
+        sys_exit("Unsupported file type %r" % seq_format)
     #Now do the renaming
     count = 0
     renamed = 0
--- a/tools/seq_rename/seq_rename.xml	Thu Nov 27 08:20:54 2014 -0500
+++ b/tools/seq_rename/seq_rename.xml	Wed May 13 06:38:43 2015 -0400
@@ -1,18 +1,18 @@
-<tool id="seq_rename" name="Rename sequences" version="0.0.6">
+<tool id="seq_rename" name="Rename sequences" version="0.0.7">
     <description>with ID mapping from a tabular file</description>
     <requirements>
         <requirement type="package" version="1.62">biopython</requirement>
         <requirement type="python-module">Bio</requirement>
     </requirements>
-    <version_commmand interpreter="python">seq_rename.py --version</version_commmand>
-    <command interpreter="python">
-seq_rename.py $input_tabular $old_column $new_column $input_file $input_file.ext $output_file
-    </command>
     <stdio>
         <!-- Anything other than zero is an error -->
         <exit_code range="1:" />
         <exit_code range=":-1" />
     </stdio>
+    <version_commmand interpreter="python">seq_rename.py --version</version_commmand>
+    <command interpreter="python">
+seq_rename.py $input_tabular $old_column $new_column $input_file $input_file.ext $output_file
+    </command>
     <inputs>
         <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file" help="FASTA, QUAL, FASTQ, or SFF format." />
         <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/>
@@ -20,7 +20,7 @@
         <param name="new_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing new sequence identifiers"/>
     </inputs>
     <outputs>
-        <data name="output_file" format="input" metadata_source="input_file" label="Renamed ${on_string}"/>
+        <data name="output_file" format_source="input_file" metadata_source="input_file" label="Renamed ${on_string}"/>
     </outputs>
     <tests>
         <test>