changeset 1:c0eb0e5792f3 draft

v0.0.2; internal changes for packaging

--- a/tools/seq_composition/README.rst	Tue Nov 18 10:01:27 2014 -0500
+++ b/tools/seq_composition/README.rst	Wed May 13 10:49:27 2015 -0400
@@ -1,7 +1,7 @@
 Galaxy tool reporting sequence composition
 ==========================================
 
-This tool is copyright 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).
 
@@ -58,6 +58,8 @@
 ------- ----------------------------------------------------------------------
 v0.0.1  - Initial version.
         - Tool definition now embeds citation information.
+v0.0.2  - Reorder XML elements (internal change only).
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
 ======= ======================================================================
 
 
@@ -67,25 +69,34 @@
 This script and related tools are being developed on this GitHub repository:
 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition
 
-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)::
 
-    $ tar -czf seq_composition.tar.gz tools/seq_composition/README.rst tools/seq_composition/seq_composition.py tools/seq_composition/seq_composition.xml tools/seq_composition/tool_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.seq_composition.tabular test-data/ecoli.fastq test-data/ecoli.seq_composition.tabular test-data/MID4_GLZRM4E04_rnd30_frclip.sff test-data/MID4_GLZRM4E04_rnd30_frclip.seq_composition.tabular
+    $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/seq_composition/
+    ...
+
+or::
 
+    $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/seq_composition/
+    ...
 
-Check this worked::
+To just build and check the tar ball, use::
 
-    $ tar -tzf seq_composition.tar.gz
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/seq_composition/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
+    test-data/MID4_GLZRM4E04_rnd30_frclip.sff
+    test-data/MID4_GLZRM4E04_rnd30_frclip.seq_composition.tabular
+    test-data/ecoli.fastq
+    test-data/ecoli.seq_composition.tabular
+    test-data/four_human_proteins.fasta
+    test-data/four_human_proteins.seq_composition.tabular
     tools/seq_composition/README.rst
     tools/seq_composition/seq_composition.py
     tools/seq_composition/seq_composition.xml
     tools/seq_composition/tool_dependencies.xml
-    test-data/four_human_proteins.fasta
-    test-data/four_human_proteins.seq_composition.tabular
-    test-data/ecoli.fastq
-    test-data/ecoli.seq_composition.tabular
-    test-data/MID4_GLZRM4E04_rnd30_frclip.sff
-    test-data/MID4_GLZRM4E04_rnd30_frclip.seq_composition.tabular
 
 
 Licence (MIT)

--- a/tools/seq_composition/seq_composition.py	Tue Nov 18 10:01:27 2014 -0500
+++ b/tools/seq_composition/seq_composition.py	Wed May 13 10:49:27 2015 -0400
@@ -21,7 +21,7 @@
 
 from Bio import SeqIO
 
-def stop_err(msg, err=1):
+def sys_exit(msg, err=1):
     sys.stderr.write(msg.rstrip() + "\n")
     sys.exit(err)
 
@@ -58,9 +58,9 @@
     sys.exit(0)
 
 if not (options.fasta or options.fastq or options.sff):
-    stop_err("Require an input filename")
+    sys_exit("Require an input filename")
 if not options.output:
-    stop_err("Require an output filename")
+    sys_exit("Require an output filename")
 
 
 file_count = 0

--- a/tools/seq_composition/seq_composition.xml	Tue Nov 18 10:01:27 2014 -0500
+++ b/tools/seq_composition/seq_composition.xml	Wed May 13 10:49:27 2015 -0400
@@ -1,9 +1,14 @@
-<tool id="seq_composition" name="Sequence composition" version="0.0.1">
+<tool id="seq_composition" name="Sequence composition" version="0.0.2">
     <description>Count bases or amino-acids</description>
     <requirements>
         <requirement type="package" version="1.64">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">seq_composition.py --version</version_command>
     <command interpreter="python">
 seq_composition.py -o "$output_file"
@@ -12,11 +17,6 @@
 --$i.ext "${i}"
 #end for
     </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" multiple="true" label="Sequence file" help="FASTA, FASTQ, or SFF format." />
     </inputs>